Diagnosing and Grading Gliomas Using a Proteomics

ABSTRACT

The present invention provides for a proteomic approach to grading gliomas, and for predicting patient survival. In addition to employing global protein expression patterns, such as by mass spectrometry, particular target proteins whose expression is altered in various gliomas can be used to predict the stage/classification of a glioma, as well as to indicate whether a given patient will be a short- or long-term survivor.

This application claims benefit of priority to U.S. ProvisionalApplication Ser. No. 60/697,083, filed Jul. 5, 2005, the entire contentsof which are hereby incorporated by reference.

The government owns rights in the invention pursuant to funding from theNIH/NIGMS (GM 58008) and NIH/NCI/NIDA (CA 86243).

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates generally to the fields of protein biologyand oncology. More particularly, it concerns the classification ofgliomas based on the expression of various proteins identified asrelevant to various glioma states.

2. Description of Related Art

Gliomas are complex cancers with different growth characteristics andinvolves different types of cells. Because the original clone of tumorcells may exist at any stage during the cell differentiation, theboundaries between cell lineages can be blurred. The currentmorphologically-based tumor classifications often mix cell lineagefeatures with tumor growth characteristics. The results are subjectiveand there can be disagreements among physicians as to what kind of tumorcell is involved. To date, a successful application of gene-basedclassification has not been applied to gliomas.

Molecular biology provides the potential for an improved method of tumorcell classification. This is based on the premise that all cellphenotypes have their origin in genetics. Thus, the rationale is that adetailed examination of gene expression will be the most accuraterepresentation of a cell's character. Recent successes in thesubclassification of neoplasms within a disease group using geneexpression profiles provide support for such a belief (Golub et al.,1999; Alizadeh et al., 2000; Bittner et al., 2000).

Thus, the issue is how to best identify the “strong” feature genes thatare closely linked to specific phenotypes from among the thousands ofgenes in gene expression profiles, and whether this information reallyaids classification of tumors more. There are many technical challengesin the path to accomplishing the task of finding the key links.Algorithms can assist in the identification of robust classifiers fromvery limited data sets. Three criteria have to be met: (a) given a setof variables, a classifier from the sample data should provide goodclassification over the general population; (b) the analysis should beable to estimate the error of a designed classifier when data arelimited; and (c) given a large set of potential variables, the analysisshould be able to select a set of variables as inputs to the classifierfrom the large number of expression level determinations provided bymicroarrays.

However, a major roadblock is the small sample size issue inherent tomicroarray-based classification efforts (Dougherty, 2001). Contributingto this are the limited numbers of human tissues for study and the costof such gene expression profiling projects. Because classifiers aredesigned from observed expression vectors that have randomness arisingfrom both biologic and experimental variability, the design, performanceevaluation, and application of classifiers must take this randomnessinto account, especially when the number of samples (tissue specimens)is small, which is the case in most human tissue-based microarraystudies.

SUMMARY OF THE INVENTION

Thus, in accordance with the present invention, there is provided amethod of diagnosing or grading a glioma comprising (a) subjecting atissue to mass spectrometry; (b) obtaining a mass spectrometric proteinprofile from the tissue; (c) comparing the mass spectrometric proteinprofile to a known profile; and (d) diagnosing or grading the tissuebased on the similarities and differences between the mass spectrometricprotein profile and the known profile. The mass spectrometry may besecondary ion mass spectrometry, laser desorption mass spectrometry,matrix assisted laser desorption mass spectrometry, or electrospray massspectrometry. The method may further comprise obtaining the tissue froma patient, and may further comprise making a treatment decision for apatient from which the tissue was obtained.

The diagnosis may comprise distinguishing non-tumor from grade I, gradeII, grade III or grade IV glioma; distinguishing grade I from grade II,grade III or grade IV glioma; distinguishing grade II from grade I,grade III or grade IV glioma; distinguishing grade III from grade I,grade II or grade IV glioma; or distinguishing grade IV from grade I,grade II, or grade III. The method may further comprise assessing one ormore patient variables, such as age, gender, extent of tumor resection,use of pre-surgery chemotherapy, or use of pre-surgery radiotherapy. Theknown profile may be is a known glioma profile and/or a normal tissueprofile. The method may further comprising performing a massspectrometric analysis of a known glioma tissue and/or of a known normaltissue.

The method may further comprise performing histologic analysis on thetissue. The method may further comprise making a prediction of patientsurvival based on the grading. The method may further comprise making aprediction of drug efficacy based on the grading. The method may furthercomprising making a decision on drug dosing based on the grading. Themethod may further comprise making a prediction of patient survivalbased on the grading.

In another embodiment, there is provided a method of diagnosing orgrading a glioma comprising (a) assessing glioma tissue for expressionof one or more of calcyclin, dynein light chain 2, calpactin I lightchain, astrocytic phosphoprotein PEA-15, fatty acid binding protein 5and tubulin-specific chaperone A; (b) comparing the expression to aknown tissue; and (c) grading the glioma based on the similarities anddifferences between the expression in the glioma and the known tissue.Assessing may comprise immunodetection, 2-D gel electrophoresis, or massspectrometry, the mass spectrometry including secondary ion massspectrometry, laser desorption mass spectrometry, matrix assisted laserdesorption mass spectrometry, or electrospray mass spectrometry.

The method may further comprise obtaining the glioma tissue from apatient. The method may also further comprise making a treatmentdecision for a patient from which the glioma tissue was obtained, suchas a decision involving predicting drug efficacy and or drug dosing. Thediagnosis may comprise distinguishing non-tumor from grade I, grade II,grade III or grade IV glioma; distinguishing grade I from grade II,grade III or grade IV glioma; distinguishing grade II from grade I,grade III or grade IV glioma; distinguishing grade III from grade I,grade II or grade IV glioma; or distinguishing grade IV from grade I,grade II, or grade III.

The method may further comprise assessing one or more patient variables,such as age, gender, extent of tumor resection, use of pre-surgerychemotherapy, or use of pre-surgery radiotherapy. The known tissue maybe a known glioma tissue, and the method may also further compriseassessing the known glioma tissue for expression of one or more ofcalcyclin, dynein light chain 2, calpactin I light chain, astrocyticphosphoprotein PEA-15, fatty acid binding protein 5 and tubulin-specificchaperone A. The known tissue may also be a known normal tissue, and themethod may also comprise assessing the known normal tissue forexpression of one or more of calcyclin, dynein light chain 2, calpactin1 light chain, astrocytic phosphoprotein PEA-15, fatty acid bindingprotein 5 and tubulin-specific chaperone A. The method may furthercomprise performing histologic analysis on the tissue. The method mayfurther comprise making a prediction of patient survival based on thegrading.

It is contemplated that any method or composition described herein canbe implemented with respect to any other method or composition describedherein.

The use of the word “a” or “an” when used in conjunction with the term“comprising” in the claims and/or the specification may mean “one,” butit is also consistent with the meaning of “one or more,” “at least one,”and “one or more than one.”

It is contemplated that any embodiment discussed in this specificationcan be implemented with respect to any method or composition of theinvention, and vice versa. Furthermore, compositions and kits of theinvention can be used to achieve methods of the invention.

Throughout this application, the term “about” is used to indicate that avalue includes the inherent variation of error for the device, themethod being employed to determine the value, or the variation thatexists among the study subjects.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and areincluded to further demonstrate certain aspects of the presentinvention. The invention may be better understood by reference to one ormore of these drawings in combination with the detailed description ofspecific embodiments presented herein.

FIG. 1: Schematic of method. Protein profiles were collected directlyfrom tissue sections and analyzed using classification programs forprognostic specific patterns. Tissue sections from tumor samples arecollected and thawed onto MALDI target plates. Subsequent sections arecollected for histological staining and analysis. Multiple matrixdroplets are deposited on each section and each droplet region isanalyzed by MALDI MS. Collected spectra are processed and the resultingpeak lists are used in a classification analysis.

FIG. 2: Protein profile generated from direct MS analysis of a matrixdroplet deposited on a 12 μm human glioma section. The intensity scalehas been expanded to display low intensity ion signals. The inset,displaying the ink range 6000 to 8000, demonstrates the complexity ofthe data collected from tissue samples. Over thirty ion signals can berecognized in the inset alone; over 500 signals were observed across theentire spectrum.

FIGS. 3A-C: Hierarchical cluster analysis of normal brain and tumortissues. (FIG. 3A) NT vs. T, (FIG. 3B) NT vs. T_(IV) and (FIG. 3C)T_(II) vs. T_(IV) tissues in the training cohort were clusteredaccording to the protein expression patterns determined by WFCCManalysis. Clustering was based on 28, 41, and 17differentially-expressed protein signals, respectively. Each rowrepresents an individual protein signal, characterized by a uniqueprotein ID number (shown on the right), and each column represents anindividual patient tissue sample. The dendrogram at the top clusterstissue samples based on similarity in protein expression profiles.Protein signal expression is characterized by cell color. Black reflectssignal absence while red reflects signal presence; increasing signalintensity is denoted by an increasing red pixel scale. N=non-tumor,T_(II)=grade II tumor and T_(IV)=grade IV tumor.

FIGS. 4A-B: Kaplan-Meier survival curves and correspondingdiscriminatory mass signals for patient groups with a short-term orlong-term prognosis according to MS proteomic patterns. Analyses wereperformed based on patient survival trends for (FIG. 4A) all gliomapatients from the time of initial pathological diagnosis using 24protein signals and (FIG. 4B) patients with grade IV glioblastoma fromthe time of GBM presentation using 2 protein signals.

FIGS. 5A-C: Immunohistochemical staining for PEA-15 validates biomarkeridentification. Two human glioma samples, a grade II astrocytoma and agrade IV glioblastoma multiforme were sectioned and analyzed tocorrelate MALDI MS protein profiling with PEA-15 immunohistochemicalstaining. Fluorescent immunohistochemical images collected from a (FIG.5A) grade II astrocytoma and (FIG. 5B) grade IV glioblastoma afterstaining for PEA-15 are presented. Mass spectrometric profiles collectedby direct-tissue MALDI MS analysis of serial glioma tissue sections arealso displayed (FIG. 5C); the protein profiles from the grade II glioma(red trace) and the grade IV glioma (blue trace) are presented. Theintensity of m/z signal 15035, identified in glioma cell lines asPEA-15, is increased in the MS profiles obtained from grade II ascompared to grade IV gliomas. Images from serial tissue sections,stained with anti-PEA-15, corroborate this by demonstrating a strongerPEA-15 staining pattern in the grade II tumor specimen as compared tothe grade IV sample.

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

Gliomas are the most common malignant primary brain tumors. These tumorsare derived from neuroepithelial cells and can be divided into twoprincipal lineages: astrocytomas and oligodendrogliomas. Current gliomaclassification schemes are based on morphologic feature assessment andremain highly subjective and problematic. Diagnoses are often dependenton the relative weighting of specific morphologic features by individualpathologists.

The present inventor used direct tissue profiling by MALDI MS to analyzethe protein patterns within human gliomas and correlate these patternsto tumor classification and patient survival. These data can be used todistinguish tumor tissue from non-tumor brain tissue, define proteinprofiles specific to tumor grade, and identify differential patientsurvival patterns based on protein expression patterns.

Since the accepted standard for glioma classification ishistopathological grading, the inventor initially sought to validate theMS approach by identifying grade-specific biomarkers that correlated tohistopathologically-determined classifications. Tumors weresub-classified by two neuropathologists, blinded to the originaldiagnosis, and analyzed by MALDI MS without knowledge of the originalclassification. Only samples with coincident clinical diagnoses wereincluded in the analysis. Based on two independent classificationapproaches, WFCCM and SDA, MALDI MS provided specific proteomic patternsthat classified glial tumors and non-tumor brain tissue with highaccuracy and precision. Proteomic profiles were used to discriminatebetween normal brain tissue and gliomas>92% of the time, with individualclassification accuracies between normal tissues and individual gradesranging from 92-100%. In addition, MALDI MS patterns were used todistinguished glioma grades with high accuracy, ranging from 76-97%. Themost difficult distinction was between WHO grade II and grade IIItumors, which mimics the clinical situation. Statistical analysisidentified over 100 potential, tumor-specific biomarkers. Validation ofMS-based tumor classification using two different statistical techniqueshighlights the power of protein profiling for tissue characterization,independent of the analysis approach.

WFCCM was also applied to identify MS-derived protein patterns thatcorrelate to patient survival trends for all glioma patients and for asubgroup of patients with histologically-confirmed GBM. For allpatients, standard treatment regimens were followed including surgicaltumor resection plus adjuvant radiotherapy and chemotherapy, asclinically-indicated and tolerated. The inventor demonstrated that arelatively small number of proteins can be used to distinguish betweenshort-term and long-term survival patients within the glioma patientpopulation as a whole (P<0.0001). While these results are in line withprevious clinical and pathological studies, demonstrating that the WHOgrading system possesses discriminating predictive power, the proteinpattern was an independent indicator of patient survival.

In addition, MALDI MS protein profiling was used to analyze a largegroup of patients with the most malignant form of glioma, GBM, and foundthat the MS pattern from two m/z signals could further stratify patientsinto a short-term and long-term survival group (P<0.0001). For bothanalyses, the MALDI MS profile was the strongest determinant of survivalin both univariate and multi-variate analyses, stronger than mostpreviously-identified predictive variables such as age, extent ofresection, tumor grade, and use of adjuvant therapy. As expected, forthe full glioma population some overlap exists between grade specificbiomarkers and the survival markers. Of the 24 discriminatory patientsurvival biomarkers for the entire glioma population, 17 were unique tothe survival stratification. On the other hand, analysis of the GBMpopulation determined two unique markers that segregated the STS and LTSpatients. These results suggest a novel approach to tissueclassification based not on histopathological features requiring visualanalysis but on a molecular analysis of the protein patterns specific tothe tissue sample.

Based on statistical analysis, a number of discriminatory proteins wereidentified including calcyclin, dynein light chain 2, calpactin I lightchain, astrocytic phosphoprotein PEA-15, fatty acid binding protein 5and tubulin-specific chaperone A. The mass spectrometric signals fromthese proteins serve to discriminate gliomas from normal brain tissueand tumors of differing grade from one another; calcyclin and dyneinlight chain 2 also discriminated between glioma survival subgroups.These proteins are thought to be involved in several aspects oftumorigenesis. Calcyclin (S100A6), which plays a potential role in cellcycle progression and cell differentiation (Toini et al., 1995), isoverexpressed in many tumors, especially at the margins of invasivecancers (Camby et al, 1999; Komatsu et al., 2002; Bronckart et al.,2001; Stulik et al., 2000). Dynein light chain 2, a subunit of themicrotubule-associated dynein motor complex, binds and sequesters Bim, aproapoptotic protein, to negatively regulate its apoptotic function(Puthalakath et al., 1999). Calpactin I light chain (p11, S100A10) isexpressed in many cancer cell lines (Zhi et al., 2003; El-Rifai et al.,2002) and is thought to bind and stimulate plasminogen conversion toplasmin, a cell surface proteinase involved in tumor cell invasion andmetastasis (Zhang et al., 2004). PEA-15, an apoptosis inhibitor involvedin several cell growth pathways (Condorelli et al., 1999; Ramos et al.,2000), is overexpressed in several tumor cell lines including breast,larynx, cervix and skin (Ramos et al., 2000; Condorelli et al., 1998)while studies have suggested overexpression of the fatty acid bindingprotein 5 gene in prostate cancer tissue and cell lines (Vaarala et al.,2000). Tubulin specific chaperone A is a cofactor required for properβ-tubulin folding (Melki et al., 1996).

Identification of these proteins was performed in both a humanglioblastoma cell line as well as a human glioblastoma tissue sample.These studies demonstrated that, while cell lines are not ideal sourcesfor protein identification, due to potential posttranslationalmodifications and genomic mutations specific to the cell lines, apositive correlation between the proteins identified from a cell lineversus a tissue sample can exist. The identification of proteins fromcell lines followed by further characterization of these proteins usingtraditional immunohistochemistry methods in intact tissues should serveas a valuable tool for protein identification and biomarker validationwhen resources are limited.

This analysis has several potential limitations. A rank cut-off was usedin WFCCM to determine the number of protein signals used in eachclassification. Therefore, the number of peaks reported is based not onthe smallest or largest number of signals that could discriminate theclasses, but rather on an intermediate number based on statisticalevidence. It may be possible to achieve a similar classification rateusing a different subset of peaks. While a variety of variables couldlead to the misclassified samples, potential limitations include thediffuse cellular nature of the tumors as well as histopathologicalinaccuracy. Furthermore, the tumors were not analyzed for geneticalterations suspected of playing a role in gliomagenesis, which may haveprognostic significance, nor did we control for histological homogeneityor require a specific treatment regimen. While it may have been usefulto focus this study on a homogeneous study population, the mixed natureof the tumors more faithfully corresponds to the clinical situation.

In summary, MALDI MS protein profiling has been used to determineprotein expression patterns that distinguish primary gliomas from normalbrain tissue, and one grade of gliomas from another, with highsensitivity and specificity. In addition, the inventor has demonstratedthat a small subset of protein signals can be used to predict survivalof glioma patients, as well as to identify differential survivalpatterns within a more homogenous population of GBM patients. SinceMALDI MS technology is capable of analyzing numerous samples, withanalysis times of approximately five minutes per sample, this technologyis amenable to high-throughput tissue screening in a clinical setting.

I. Gliomas

Gliomas are a diverse group of brain tumors that arise from the normal“glial” cells of the brain. The most important determinant of survivalfor gliomas is the “grade” of the glioma. The low-grade gliomas have aprotracted natural history, while the high grade gliomas (anaplasticastrocytoma and glioblastoma multiforme) are much more difficult tosuccessfully treat. The gliomas have specific signs and symptoms thatare primarily related to the location of the glioma.

The temporal lobe gliomas, for example, may cause epilepsy, difficultywith speech or loss of memory. The frontal lobe gliomas may causebehavioral changes, weakness of the arms or legs or difficulty withspeech. The occipital gliomas may cause loss of vision. The parietalgliomas may cause loss of spatial orientation, diminished sensation onthe opposite side of the body, or inability to recognize once familiarobjects or persons.

Grading according to degree of malignancy was first proposed in 1949. Inthis classification, astrocytomas and glioblastomas represent differentgrades of malignancy of the same tumor. Grade I tumors, typically slowgrowing, are characterized by most cells having normal characteristics,and few mitotic features. Endothelial proliferation is absent. Grade IItumors, previously designated “astroblastomas,” are characterized by anincreased number of cells with polymorphic nuclei in mitoses. There isno clear line of demarcation from normal tissue. Grade III tumorsrepresent anaplastic astrocytomas and Grade IV tumors represent thetypical glioblastoma multiforme, characterized by cellular pleomorphism,vascular proliferation, mitoses, and multinucleated giant cells.

Surgery. The role of surgical resection in the treatment of malignantgliomas remains controversial even after 75 years of experience withprimary malignant gliomas. Surgery permits a pathologic diagnosis to beestablished while the patient is still alive. However, many physiciansargue that current radiologic imaging methods, including computedtomography (CT) and magnetic resonance imaging (MRI), permit a malignantbrain tumor to be diagnosed without the necessity for attempted tumorresection and, thus, avoid the risks of surgery.

There is evidence that surgical reduction of tumor to very smallresidual amounts can prolong survival and permit patients to return toactive lives. However, retrospective studies are subject to thecriticism that the extent of attempted resection depends on thecondition of the patient at the time of surgery (age, tumor location,clinical state), and that favorable conditions usually lead the surgeonto attempt a greater resection. Therefore, in such studies, it is notclear that the extent of surgery is as important to survival as are themore favorable prognostic variables. Nevertheless, these results supportthe surgical removal of the largest possible tumor volume that can bedone safely. Patients are frequently able to return to a full, activelife without the need for large doses of corticosteroids to ameliorateincapacitating symptoms.

Radiation. The proper portals and doses of radiation for brain tumorshave changed with the advent of better imaging techniques. It has beenreported in controlled studies that postoperative whole-brain radiationtherapy increases patient survival over surgery alone. Other data showedthat patients receiving 5,500 to 6,000 cGy of radiation livesignificantly longer than those receiving 5,000 cGy.

Prolonged survival has been reported in patients with recurrentmalignant gliomas who were treated with temporarily implanted I¹²⁵sources. A phase III trial randomized newly diagnosed patients toreceive either (a) postoperative temporary I¹²⁵ seed implantation in theresidual tumor bed, followed by standard external-beam radiotherapy plusIV BCNU; or (b) external radiotherapy plus BCNU, without seedimplantation. Preliminary review of the results demonstrated thatpatients who received I¹²⁵ seeds lived longer than those who did notreceive seeds, although the difference did not quite reach statisticalsignificance. The study suggests but does not prove that brachytherapyextends survival beyond that achievable with external radiotherapyalone.

Radiosurgery. Radiosurgery, either by gamma knife or linear accelerator,has been shown to be effective in the treatment of arteriovenousmalformations, small primary and metastatic brain tumors, and benignbrain tumors, such as meningiomas and acoustic neuromas. Itsinvestigational use in the treatment of gliomas has been addressed inseveral reports. In one trial, 37 patients received radiosurgery (1,000to 2,000 cGy) to residual contrast-enhancing tumor after treatment withconventional external-beam radiation therapy. Local recurrence stilloccurred, but overall survival time may have been prolonged. Of the 37patients, 7 (19%) required reoperation at a median time of 5 monthsafter radiosurgery to remove necrotic tumor.

A major problem with radiosurgery (as with brachytherapy) is bias in theselection of patients for treatment. However, radiosurgery may be ofbenefit in a small group of good-prognosis patients with small tumors.

Chemotherapy. In 1983, it was reported that surgery plus radiationtherapy and BCNU chemotherapy significantly adds to the survival ofpatients with malignant glioma, as compared with surgery plus radiationtherapy without chemotherapy. High-dose methylprednisolone does notprolong survival. Both procarbazine and streptozotocin have demonstratedeffectiveness similar to that of BCNU. BCNU alone is as effective asBCNU followed by procarbazine, or BCNU plus hydroxyurea followed byprocarbazine plus teniposide. Methotrexate also has been reported to beeffective in treating gliomas.

Intra-arterial BCNU is no more effective than intravenous BCNU andsubstantially more toxic. Serious toxicity induced by intra-arterialBCNU included irreversible encephalopathy and/or visual loss ipsilateralto the infused carotid artery. In the same study, fluorouracil did notinfluence survival. Neuropathologically, intra-arterial BCNU producedwhite matter necrosis. Intra-arterial cisplatinum is safer than BCNUadministered by the same route but is no more effective than anothernitrosourea, PCNU.

Over the past several years, there has been increasing interest in theuse of targeted interstitial drug delivery using biodegradablemicrospheres and wafers. In a multicenter controlled trial, 222 patientswith recurrent malignant gliomas who required reoperation were randomlyassigned to receive surgically implanted biodegradable polymer discscontaining 3.85% of BCNU or discs containing placebo. Median survival ofthe 110 patients who received BCNU polymers was significantly longerthan that of the 112 patients who received placebo polymers (31 versus23 weeks).

In addition to these controlled survival-based clinical trials, a largenumber of agents have also been tested in response-based studies inglioma patients. To date, however, no drug has been found to be moreeffective than the nitrosoureas. The combination of procarbazine, CCNU,and vincristine (PCV) has become a popular chemotherapeutic regimen formalignant glioma, and may be more effective than BCNU alone.

1. Glioblastoma Multiforme

Glioma-glioblastoma multiforme (GBM), referred to a Grade IV glioma, isthe most malignant of the neuroepithelial neoplasms, characterized bycellular pleomorphism, numerous mitotic figures, and oftenmultinucleated giant cell. Proliferation of the vascular endothelium isseen as well as areas of necrosis with circumjacent pseudopalisading ofthe neoplastic cells. It can appear as either a well-circumscribedglobular mass or a more diffuse mass lesion. The cut surface revealsnecrosis, fatty degeneration, and hemorrhage. Hemorrhages have beenfound in 40%, with necrosis in up to 52% of the cases. The tumor isusually solid, although cysts may be present. Rarely the tumor consistsof a solitary cyst and mural nodule.

Glioblastoma multiforme constitutes approximately 7% of childhoodintracranial neoplasms. The overall male to female ratio in children is3:2. In adults, glioblastomas are noted most frequently in the frontallobe with the temporal lobe second in frequency. Childhood glioblastomasof the cerebral hemispheres are also located most often in the frontallobe; with the second most frequent site being the parietal lobe.Primary glioblastoma of the spinal cord in childhood is rare.

Glioblastoma multiforme in children appears to have two characteristiccourses, each of which is related to the location of the tumor.Glioblastomas of the brainstem, a more primitive part of the centralnervous system, occur at a younger age and have a shorter mean survivalrelative to those of the cerebral hemispheres. Glioblastoma multiformeof the cerebral hemisphere, a more highly developed part of the centralnervous system, is characterized by onset in older children (13 years)and by a longer mean survival.

Headache is the most common complaint and papilledema the most commonphysical finding in children with hemispheric glioblastoma. Seizures arenoted in up to one third of the children. Survival rates in patientswith glioblastoma multiforme is uniformly poor. In studies of childrentreated with surgery and intracranial radiation, only one third of thechildren are alive one year after diagnosis. Survival of children withglioblastoma multiforme of either of the cerebral hemispheres or thebrainstem has significantly increased since the advent of dexamethasonetherapy. Presently therapy consists of surgery plus combinationchemotherapy.

In summary it can be said that glioblastoma multiforme behaves similarlyin both children and adults. The course of intracranial glioblastomas inchildren is more rapidly fatal than that of other similarly situatedgliomas in childhood. While the overall survival rate is very poor inpatients with a glioblastoma multiforme, intensive chemotherapy withsurgical resection does offer some hope in increasing survival timeamong children.

2. Astrocytoma

Astrocytomas are tumors that arise from brain cells called astrocytes.Gliomas originate from glial cells, most often astrocytes. Sometimes theterms “astrocytoma” and “glioma” are used interchangeably. Astrocytomasare of two main types—high-grade and low-grade. High-grade tumors growrapidly and can easily spread through the brain. Low-grade astrocytomasare usually localized and grow slowly over a long period of time.High-grade tumors are much more aggressive and require very intensetherapy. The majority of astrocytic tumors in children are low-grade,whereas the majority in adults are high-grade. These tumors can occuranywhere in the brain and spinal cord. Common sites in children are thecerebellum (the area just above the back of the neck), cerebralhemispheres (the top part of the brain), and the thalamus orhypothalamus (located in the center of the brain).

Astrocytomas account for the majority of pediatric brain tumors. About700 children are diagnosed with low-grade astrocytomas each year. Inchildren, about 90 percent of astrocytomas are low-grade; only about 10percent are high-grade.

Clinical features and symptoms depend on the location of the tumor andthe child's age. The most common location is the cerebellum. Patientswith cerebellar tumors have symptoms that include headache, vomiting andunsteadiness in walking. Tumors in the cerebral hemispheres commonlypresent with seizures: occasionally there is weakness of the arms andlegs. Tumors in the hypothalamus often present with visual problems,while thalamic tumors cause headaches and arm or leg weakness.

Complete surgical removal of the tumor (resection) is the best optionfor tumors in areas where this can be done without damaging the normal,surrounding brain. For low-grade astrocytomas that are completelyremoved, further therapy is usually not needed. If the surgeon cannotcompletely remove the tumor, chemotherapy or radiation therapy may begiven. The choice of treatments depends on the age of the patient, tumorlocation; some patients may even be followed without treatment.Radiation therapy is used for older children and those whose tumors keepgrowing despite chemotherapy. About 90 percent of children withlow-grade astrocytomas are alive five years from diagnosis.

High-grade astrocytomas can rarely be removed totally because they oftenaffect large areas of the brain by the time symptoms are obvious. Allpatients with high-grade astrocytomas usually receive chemotherapyregardless of age. Most, except the very youngest, also receiveradiation therapy. Currently, the prognosis is poor in the group ofpatients. The subset of patients who have high-grade tumors that can beremoved may have survival rates of 35 to 40 percent after postsurgicalirradiation with chemotherapy. The survival of other patients is verypoor.

Research efforts for the low-grade astrocytomas focus on developingchemotherapy regimens that control tumor growth with fewer side effectson other organs of the body. Because these tumors grow slowly, thestrategy is to give less intensive chemotherapy over longer periods oftime. For older children and those whose tumors progress despitechemotherapy, new radiation techniques are under study to deliver morelocalized therapy with minimal effects on the normal brain.

For high-grade tumors, new approaches include use of new chemotherapydrugs, and the potential option of high doses of chemotherapy.Investigational new approaches, including new chemotherapy drugs andgene therapy to help protect the bone marrow from the side effects sothat more intensive chemotherapy can be given are in various stages ofdevelopment.

3. Oligodendroglioma and Anaplastic Oliogodendroglioma

Oligodendrogliomas are believed to be tumors of cells calledoligodendrocytes that have a role in the structure and function of thebrain. However, the origins of these tumor cells has been questioned.Oligodendrogliomas are classified as low grade oligodendroglioma (lessaggressive) and anaplastic oligodendroglioma (more aggressive). Morecommon that pure oligodendrogliomas are low grade and anaplastic tumorsthat are a mixture of astrocytoma and oligodendroglioma(“oligoastrocytomas”).

The initial treatment of low grade oligodendroglioma andoligoastrocytoma consists of maximal surgery. The role of radiationtherapy has been disputed, but younger people with minimal residualdisease after surgery may have radiation therapy deferred as long asthere is adequate monitoring of the tumor by MRI or CT scanning.

Anaplastic oligodendrogliomas and mixed oligoastrocytomas are moresensitive to chemotherapy than astrocytomas. A high rate of response tothe use of PCV (procarbazine, CCNU, vincristine) chemotherapy has madethe use of chemotherapy prior to radiation therapy the standard of carefor these tumors. The actual effectiveness of this treatment regimen iscurrently being investigated in a large multinational trial.

Additionally, low grade oligodendrogliomas are also sensitive tochemotherapy, and PCV can be used when low grade tumors begin to growdespite prior radiation therapy.

II. Glioma-Related Genes and their Classification

As discussed above, the present invention provides a protein-basedclassification of gliomas. This classification is based on theidentification of six particular proteins, the expression of whichcorrelates with the various glioma disease states. Using informationderived from these six targets, one can grade a glioma. The six proteinsare calcyclin, dynein light chain 2, calpactin I light chain, astrocyticphosphoprotein PEA-15, fatty acid binding protein 5 and tubulin-specificchaperone A.

1. Calcyclin

A member of the S100 family of calcium binding proteins, calcyclin in isA prolactin receptor-associated protein, one of a family of small(around 10 kD) calcium-binding proteins containing the EF-hand motif,originally isolated from Erlich ascites tumour cells, but human and ratforms now identified. It is regulated through the cell cycle and bindsto annexin II (p36) and to glyceraldehyde-3-phosphate dehydrogenase. Insitu hybridization shows that, in mouse, calcyclin transcripts arerestricted to specific cell types within a limited number of organs.High levels of expression in the epithelia lining the gastrointestinal,respiratory and urinary tracts, and specific localization of thetranscripts to the goblet cells in the small intestine, lead to asuggestion for a role in the process of mucus secretion. In addition,calcyclin expression is detected in mouse corpus luteum, placenta andnerves within the gut wall, which are all sites of regulated exocytosis.

2. Calpactin I Light Chain

Calpactins are a family of related Ca²⁺-regulated cytoskeletal proteinsand, like calcyclin are a members of the S100 family of proteinscontaining EF-hand calcium-binding motifs. Comparison of the tissuedistribution of calpactin I heavy and light chains by Western blotsrevealed that these subunits are coordinately expressed. Both solubleand cytoskeletal forms of the heavy chain of calpactin I were detectedin human fibroblasts, whereas only a soluble pool of calpactin II wasfound. These two forms of the calpactin I heavy chain differed both intheir state of association with the light chain and in their rate ofturnover. Both the soluble pool of the calpactin I heavy chain andcalpactin II turned over three to four times faster than thecytoskeletal pool of heavy and light chains. Immunofluorescencemicroscopy revealed that the calpactin I light chain was presentexclusively in the cytoskeleton, whereas the calpactin I heavy chaindistribution was more diffuse. Calpactin I light chain is also known asa ligand for annexin II. This protein is designated as p11, and is codedby a human gene designated as CPL11.

3. Astrocytic Phosphoprotein PEA-15

Astrocytic phosphoprotein PEA-15 inhibits both fas- andtnfrsf1a-mediated caspase-8 activity and apoptosis. It also regulatesglucose transport by controlling both the content of slc2a1 glucosetransporters on the plasma membrane, and the insulin-dependenttrafficking of slc2a4 from the cell interior to the surface. It isassociated with microtubules, interacts with casp8/flice and fadd, andcontains 1 death effector (ded) domain.

Phosphorylated by protein kinase c and calcium-calmodulin-dependentprotein kinase, these phosphorylation events are modulated byneurotransmitters or hormones. It is ubiquitously expressed, and is mostabundant in tissues such as heart, brain, muscle and adipose tissuewhich utilize glucose as an energy source. Lower expression is observedin glucose-producing tissues, and higher levels of expression are foundin tissues from individuals with type 2 diabetes than in controls.

4. Tubulin Specific Chaperone A

Cofactor A is one of four proteins (cofactors A, D, E, and C) involvedin the pathway leading to correctly folded β-tubulin from foldingintermediates. Cofactors A and D are believed to play a role incapturing and stabilizing β-tubulin intermediates in a quasi-nativeconfirmation. Cofactor E binds to the cofactor D/β-tubulin complex;interaction with cofactor C then causes the release of β-tubulinpolypeptides that are committed to the native state.

By immunofluorescence microscopy analysis, Martin et al. (2000)demonstrated that overexpression of TBCD correlates with microtubuledepolymerization and a progressive loss of microtubules, leading to arapid drop in levels of α-tubulin but not β-tubulin. The results showedthat TBCD modulates microtubule dynamics by capturing GTP-boundβ-tubulin. The interactions did not lead to apoptosis.

5. Dynein Light Chain 2

DLC2 encodes a novel Rho-family protease with a RhoGAP domain, a SAM(sterile a motif) domain related to p73/p63, and a lipid-bindingStAR-related lipid transfer (START) domain. It is found at 13q12.3.Biochemical analysis indicates that DLC2 protein has GAP activityspecific for small GTPases RhoA and Cdc42. DLC2 is homologous to DLC1, apreviously identified tumor suppressor gene at 8p22-p21.3 frequentlydeleted in HCC.

Remarkably, mutational analysis of DLC1 and DLC2 indicates that a singlesurface residue (residue 41) determines the specific localization ofDLCs with their respective motor complexes. In vivo, DLC2 is foundexclusively as a component of the myosin V motor complex and Bmf bindsDLC2 selectively.

6. Fatty Acid Binding Protein 5

Adipocyte fatty acid binding protein FABP5 is a 15 kD member of theintracellular fatty acid binding protein (FABP) family, which is knownfor the ability to bind fatty acids and related compounds (bile acids orretinoids) in an internal cavity. The fatty acid binding proteins aP2(fatty acid binding protein [FABP]-4) and mal1 (FABP5) are closelyrelated and both are expressed in adipocytes. Absence of FABP5/mal1results in increased systemic insulin sensitivity in two models ofobesity and insulin resistance. Adipocytes isolated from mal1-deficientmice also exhibited enhanced insulin-stimulated glucose transportcapacity. In contrast, mice expressing high levels of mal1 in adiposetissue display reduced systemic insulin sensitivity.

III. Prognostic Determinations in Glioma

In addition to the glioma classification methods described above, thepresent invention also provides for making predictions on the clinicalprospects of a glioma patient. Again, the inventors have usedstatistical analysis of data to select the following set of proteinsthat are differentially regulated in various forms of glioma and thuspermit the accurate classification of each type of glioma: calcyclin,calpactin I light chain, astrocytic phosphoprotein PEA-15 andtubulin-specific chaperone A. Using information derived from thesetargets, one can predict whether a glioma patient will be a long termsurvivor or not.

IV. Protein-Based Detection Immunodetection

Thus, in accordance with the present invention, methods are provided forthe assaying of protein expression in patients suffering from gliomas.As discussed above, the principle applications of this assay are to: (a)determine what grade of glioma a given patient suffers from; and (b)determine the likelihood and extent of patient survival. In each ofthese assays, the expression of a particular set of target proteins, setforth in the preceding sections, will be measured.

There are a variety of methods that can be used to assess proteinexpression. One such approach is to perform protein identification withthe use of antibodies. As used herein, the term “antibody” is intendedto refer broadly to any immunologic binding agent such as IgG, IgM, IgA,IgD and IgE. Generally, IgG and/or IgM are preferred because they arethe most common antibodies in the physiological situation and becausethey are most easily made in a laboratory setting. The term “antibody”also refers to any antibody-like molecule that has an antigen bindingregion, and includes antibody fragments such as Fab′, Fab, F(ab)₂,single domain antibodies (DABs), Fv, scFv (single chain Fv), and thelike. The techniques for preparing and using various antibody-basedconstructs and fragments are well known in the art. Means for preparingand characterizing antibodies, both polyclonal and monoclonal, are alsowell known in the art (See, e.g., Antibodies: A Laboratory Manual, ColdSpring Harbor Laboratory, 1988; incorporated herein by reference). Inparticular, antibodies to calcyclin, calpactin I light chain, astrocyticphosphoprotein PEA-15 and tubulin-specific chaperone A are contemplated.

In accordance with the present invention, immunodetection methods areprovided. Some immunodetection methods include enzyme linkedimmunosorbent assay (ELISA), radioimmunoassay (RIA), immunoradiometricassay, fluoroimmunoassay, chemiluminescent assay, bioluminescent assay,and Western blot to mention a few. The steps of various usefulimmunodetection methods have been described in the scientificliterature, such as, e.g., Doolittle & Ben-Zeev O, 1999; Gulbis &Galand, 1993; De Jager et al., 1993; and Nakamura et al., 1987, eachincorporated herein by reference.

In general, the immunobinding methods include obtaining a samplesuspected of containing a relevant polypeptide, and contacting thesample with a first antibody under conditions effective to allow theformation of immunocomplexes. In terms of antigen detection, thebiological sample analyzed may be any sample that is suspected ofcontaining an antigen, such as, for example, a tissue section orspecimen, a homogenized tissue extract, a cell, or even a biologicalfluid.

Contacting the chosen biological sample with the antibody undereffective conditions and for a period of time sufficient to allow theformation of immune complexes (primary immune complexes) is generally amatter of simply adding the antibody composition to the sample andincubating the mixture for a period of time long enough for theantibodies to form immune complexes with, i.e., to bind to, any antigenspresent. After this time, the sample-antibody composition, such as atissue section, ELISA plate, dot blot or western blot, will generally bewashed to remove any non-specifically bound antibody species, allowingonly those antibodies specifically bound within the primary immunecomplexes to be detected.

In general, the detection of immunocomplex formation is well known inthe art and may be achieved through the application of numerousapproaches. These methods are generally based upon the detection of alabel or marker, such as any of those radioactive, fluorescent,biological and enzymatic tags. Patents concerning the use of such labelsinclude U.S. Pat. Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345;4,277,437; 4,275,149 and 4,366,241, each incorporated herein byreference. Of course, one may find additional advantages through the useof a secondary binding ligand such as a second antibody and/or abiotin/avidin ligand binding arrangement, as is known in the art.

The antibody employed in the detection may itself be linked to adetectable label, wherein one would then simply detect this label,thereby allowing the amount of the primary immune complexes in thecomposition to be determined. Alternatively, the first antibody thatbecomes bound within the primary immune complexes may be detected bymeans of a second binding ligand that has binding affinity for theantibody. In these cases, the second binding ligand may be linked to adetectable label. The second binding ligand is itself often an antibody,which may thus be termed a “secondary” antibody. The primary immunecomplexes are contacted with the labeled, secondary binding ligand, orantibody, under effective conditions and for a period of time sufficientto allow the formation of secondary immune complexes. The secondaryimmune complexes are then generally washed to remove anynon-specifically bound labeled secondary antibodies or ligands, and theremaining label in the secondary immune complexes is then detected.

Further methods include the detection of primary immune complexes by atwo step approach. A second binding ligand, such as an antibody, thathas binding affinity for the antibody is used to form secondary immunecomplexes, as described above. After washing, the secondary immunecomplexes are contacted with a third binding ligand or antibody that hasbinding affinity for the second antibody, again under effectiveconditions and for a period of time sufficient to allow the formation ofimmune complexes (tertiary immune complexes). The third ligand orantibody is linked to a detectable label, allowing detection of thetertiary immune complexes thus formed. This system may provide forsignal amplification if this is desired.

One method of immunodetection designed by Charles Cantor uses twodifferent antibodies. A first step biotinylated, monoclonal orpolyclonal antibody is used to detect the target antigen(s), and asecond step antibody is then used to detect the biotin attached to thecomplexed biotin. In that method the sample to be tested is firstincubated in a solution containing the first step antibody. If thetarget antigen is present, some of the antibody binds to the antigen toform a biotinylated antibody/antigen complex. The antibody/antigencomplex is then amplified by incubation in successive solutions ofstreptavidin (or avidin), biotinylated DNA, and/or complementarybiotinylated DNA, with each step adding additional biotin sites to theantibody/antigen complex. The amplification steps are repeated until asuitable level of amplification is achieved, at which point the sampleis incubated in a solution containing the second step antibody againstbiotin. This second step antibody is labeled, as for example with anenzyme that can be used to detect the presence of the antibody/antigencomplex by histoenzymology using a chromogen substrate. With suitableamplification, a conjugate can be produced which is macroscopicallyvisible.

Another known method of immunodetection takes advantage of theimmuno-PCR (Polymerase Chain Reaction) methodology. The PCR method issimilar to the Cantor method up to the incubation with biotinylated DNA,however, instead of using multiple rounds of streptavidin andbiotinylated DNA incubation, the DNA/biotin/streptavidin/antibodycomplex is washed out with a low pH or high salt buffer that releasesthe antibody. The resulting wash solution is then used to carry out aPCR reaction with suitable primers with appropriate controls. At leastin theory, the enormous amplification capability and specificity of PCRcan be utilized to detect a single antigen molecule.

As detailed above, immunoassays are in essence binding assays. Certainimmunoassays are the various types of enzyme linked immunosorbent assays(ELISAs) and radioimmunoassays (RIA) known in the art. However, it willbe readily appreciated that detection is not limited to such techniques,and Western blotting, dot blotting, FACS analyses, and the like may alsobe used.

In one exemplary ELISA, the antibodies of the invention are immobilizedonto a selected surface exhibiting protein affinity, such as a well in apolystyrene microtiter plate. Then, a test composition suspected ofcontaining the antigen, such as a clinical sample, is added to thewells. After binding and washing to remove non-specifically bound immunecomplexes, the bound antigen may be detected. Detection is generallyachieved by the addition of another antibody that is linked to adetectable label. This type of ELISA is a simple “sandwich ELISA”.Detection may also be achieved by the addition of a second antibody,followed by the addition of a third antibody that has binding affinityfor the second antibody, with the third antibody being linked to adetectable label.

In another exemplary ELISA, the samples suspected of containing theantigen are immobilized onto the well surface and then contacted withthe anti-ORF message and anti-ORF translated product antibodies of theinvention. After binding and washing to remove non-specifically boundimmune complexes, the bound anti-ORF message and anti-ORF translatedproduct antibodies are detected. Where the initial anti-ORF message andanti-ORF translated product antibodies are linked to a detectable label,the immune complexes may be detected directly. Again, the immunecomplexes may be detected using a second antibody that has bindingaffinity for the first anti-ORF message and anti-ORF translated productantibody, with the second antibody being linked to a detectable label.

Another ELISA in which the antigens are immobilized, involves the use ofantibody competition in the detection. In this ELISA, labeled antibodiesagainst an antigen are added to the wells, allowed to bind, and detectedby means of their label. The amount of an antigen in an unknown sampleis then determined by mixing the sample with the labeled antibodiesagainst the antigen during incubation with coated wells. The presence ofan antigen in the sample acts to reduce the amount of antibody againstthe antigen available for binding to the well and thus reduces theultimate signal. This is also appropriate for detecting antibodiesagainst an antigen in an unknown sample, where the unlabeled antibodiesbind to the antigen-coated wells and also reduces the amount of antigenavailable to bind the labeled antibodies.

“Under conditions effective to allow immune complex (antigen/antibody)formation” means that the conditions preferably include diluting theantigens and/or antibodies with solutions such as BSA, bovine gammaglobulin (BGG) or phosphate buffered saline (PBS)/Tween. These addedagents also tend to assist in the reduction of nonspecific background.The “suitable” conditions also mean that the incubation is at atemperature or for a period of time sufficient to allow effectivebinding. Incubation steps are typically from about 1 to 2 to 4 hours orso, at temperatures preferably on the order of 25° C. to 27° C., or maybe overnight at about 4° C. or so.

The antibodies of the present invention may also be used in conjunctionwith both fresh-frozen and/or formalin-fixed, paraffin-embedded tissueblocks prepared for study by immunohistochemistry (IHC). The method ofpreparing tissue blocks from these particulate specimens has beensuccessfully used in previous IHC studies of various prognostic factors,and/or is well known to those of skill in the art (Brown et al., 1990;Abbondanzo et al., 1999; Allred et al., 1990).

Also contemplated in the present invention is the use ofimmunohistochemistry. This approach uses antibodies to detect andquantify antigens in intact tissue samples. Generally, frozen-sectionsare prepared by rehydrating frozen “pulverized” tissue at roomtemperature in phosphate buffered saline (PBS) in small plasticcapsules; pelleting the particles by centrifugation; resuspending themin a viscous embedding medium (OCT); inverting the capsule and pelletingagain by centrifugation; snap-freezing in −70° C. isopentane; cuttingthe plastic capsule and removing the frozen cylinder of tissue; securingthe tissue cylinder on a cryostat microtome chuck; and cutting 25-50serial sections.

Permanent-sections may be prepared by a similar method involvingrehydration of the 50 mg sample in a plastic microfuge tube; pelleting;resuspending in 10% formalin for 4 hours fixation; washing/pelleting;resuspending in warm 2.5% agar; pelleting; cooling in ice water toharden the agar; removing the tissue/agar block from the tube;infiltrating and/or embedding the block in paraffin; and cutting up to50 serial permanent sections.

V. Protein-Based Detection Mass Spectrometry

By exploiting the intrinsic properties of mass and charge, massspectrometry (MS) can resolved and confidently identified a wide varietyof complex compounds, including proteins. Traditional quantitative MShas used electrospray ionization (ESI) followed by tandem MS (MS/MS)(Chen et al., 2001; Zhong et al., 2001; Wu et al., 2000) while newerquantitative methods are being developed using matrix assisted laserdesorption/ionization (MALDI) followed by time of flight (TOF) MS(Bucknall et al., 2002; Mirgorodskaya et al., 2000; Gobom et al., 2000).In accordance with the present invention, one can generate massspectrometry profiles that are useful for grading gliomas and predictingglioma patient survival, without regard for the identity of specificproteins. Alternatively, given the established links with calcyclin,calpactin I light chain, astrocytic phosphoprotein PEA-15 andtubulin-specific chaperone A, mass spectrometry may be used to look forthe levels of these proteins particularly.

1. ESI

ESI is a convenient ionization technique developed by Fenn andcolleagues (Fenn et al., 1989) that is used to produce gaseous ions fromhighly polar, mostly nonvolatile biomolecules, including lipids. Thesample is injected as a liquid at low flow rates (1-10 μL/min) through acapillary tube to which a strong electric field is applied. The fieldgenerates additional charges to the liquid at the end of the capillaryand produces a fine spray of highly charged droplets that areelectrostatically attracted to the mass spectrometer inlet. Theevaporation of the solvent from the surface of a droplet as it travelsthrough the desolvation chamber increases its charge densitysubstantially. When this increase exceeds the Rayleigh stability limit,ions are ejected and ready for MS analysis.

A typical conventional ESI source consists of a metal capillary oftypically 0.1-0.3 mm in diameter, with a tip held approximately 0.5 to 5cm (but more usually 1 to 3 cm) away from an electrically groundedcircular interface having at its center the sampling orifice, such asdescribed by Kabarle et al. (1993). A potential difference of between 1to 5 kV (but more typically 2 to 3 kV) is applied to the capillary bypower supply to generate a high electrostatic field (10⁶ to 10⁷ V/m) atthe capillary tip. A sample liquid carrying the analyte to be analyzedby the mass spectrometer, is delivered to tip through an internalpassage from a suitable source (such as from a chromatograph or directlyfrom a sample solution via a liquid flow controller). By applyingpressure to the sample in the capillary, the liquid leaves the capillarytip as a small highly electrically charged droplets and furtherundergoes desolvation and breakdown to form single or multicharged gasphase ions in the form of an ion beam. The ions are then collected bythe grounded (or negatively charged) interface plate and led through anthe orifice into an analyzer of the mass spectrometer. During thisoperation, the voltage applied to the capillary is held constant.Aspects of construction of ESI sources are described, for example, inU.S. Pat. Nos. 5,838,002; 5,788,166; 5,757,994; RE 35,413; and5,986,258.

2. ESI/MS/MS

In ESI tandem mass spectroscopy (ESI/MS/MS), one is able tosimultaneously analyze both precursor ions and product ions, therebymonitoring a single precursor product reaction and producing (throughselective reaction monitoring (SRM)) a signal only when the desiredprecursor ion is present. When the internal standard is a stableisotope-labeled version of the analyte, this is known as quantificationby the stable isotope dilution method. This approach has been used toaccurately measure pharmaceuticals (Zweigenbaum et al., 2000;Zweigenbaum et al., 1999) and bioactive peptides (Desiderio et al.,1996; Lovelace et al., 1991). Newer methods are performed on widelyavailable MALDI-TOF instruments, which can resolve a wider mass rangeand have been used to quantify metabolites, peptides, and proteins.Larger molecules such as peptides can be quantified using unlabeledhomologous peptides as long as their chemistry is similar to the analytepeptide (Duncan et al., 1993; Bucknall et al., 2002). Proteinquantification has been achieved by quantifying tryptic peptides(Mirgorodskaya et al., 2000). Complex mixtures such as crude extractscan be analyzed, but in some instances sample clean up is required(Nelson et al., 1994; Gobom et al., 2000).

3. SIMS

Secondary ion mass spectroscopy, or SIMS, is an analytical method thatuses ionized particles emitted from a surface for mass spectroscopy at asensitivity of detection of a few parts per billion. The sample, surfaceis bombarded by primary energetic particles, such as electrons, ions(e.g., O, Cs), neutrals or even photons, forcing atomic and molecularparticles to be ejected from the surface, a process called sputtering.Since some of these sputtered particles carry a charge, a massspectrometer can be used to measure their mass and charge. Continuedsputtering permits measuring of the exposed elements as material isremoved. This in turn permits one to construct elemental depth profiles.Although the majority of secondary ionized particles are electrons, itis the secondary ions which are detected and analysis by the massspectrometer in this method.

4. LD-MS and LDLPMS

Laser desorption mass spectroscopy (LD-MS) involves the use of a pulsedlaser, which induces desorption of sample material from a samplesite—effectively, this means vaporization of sample off of the samplesubstrate. This method is usually only used in conjunction with a massspectrometer, and can be performed simultaneously with ionization if oneuses the right laser radiation wavelength.

When coupled with Time-of-Flight (TOF) measurement, LD-MS is referred toas LDLPMS (Laser Desorption Laser Photoionization Mass Spectroscopy).The LDLPMS method of analysis gives instantaneous volatilization of thesample, and this form of sample fragmentation permits rapid analysiswithout any wet extraction chemistry. The LDLPMS instrumentationprovides a profile of the species present while the retention time islow and the sample size is small. In LDLPMS, an impactor strip is loadedinto a vacuum chamber. The pulsed laser is fired upon a certain spot ofthe sample site, and species present are desorbed and ionized by thelaser radiation. This ionization also causes the molecules to break upinto smaller fragment-ions. The positive or negative ions made are thenaccelerated into the flight tube, being detected at the end by amicrochannel plate detector. Signal intensity, or peak height, ismeasured as a function of travel time. The applied voltage and charge ofthe particular ion determines the kinetic energy, and separation offragments are due to different size causing different velocity. Each ionmass will thus have a different flight-time to the detector.

One can either form positive ions or negative ions for analysis.Positive ions are made from regular direct photoionization, but negativeion formation require a higher powered laser and a secondary process togain electrons. Most of the molecules that come off the sample site areneutrals, and thus can attract electrons based on their electronaffinity. The negative ion formation process is less efficient thanforming just positive ions. The sample constituents will also affect theoutlook of a negative ion spectra.

Other advantages with the LDLPMS method include the possibility ofconstructing the system to give a quiet baseline of the spectra becauseone can prevent coevolved neutrals from entering the flight tube byoperating the instrument in a linear mode. Also, in environmentalanalysis, the salts in the air and as deposits will not interfere withthe laser desorption and ionization. This instrumentation also is verysensitive, known to detect trace levels in natural samples without anyprior extraction preparations.

5. MALDI-TOF-MS

Since its inception and commercial availability, the versatility ofMALDI-TOF-MS has been demonstrated convincingly by its extensive use forqualitative analysis. For example, MALDI-TOF-MS has been employed forthe characterization of synthetic polymers (Marie et al., 2000; Wu etal., 1998). peptide and protein analysis (Roepstorff et al., 2000;Nguyen et al., 1995), DNA and oligonucleotide sequencing (Miketova etal., 1997; Faulstich et al., 1997; Bentzley et al., 1996), and thecharacterization of recombinant proteins (Kanazawa et al., 1999;Villanueva et al., 1999). Recently, applications of MALDI-TOF-MS havebeen extended to include the direct analysis of biological tissues andsingle cell organisms with the aim of characterizing endogenous peptideand protein constituents (Li et al., 2000; Lynn et al., 1999; Stoeckliet al., 2001; Caprioli et al., 1997; Chaurand et al., 1999; Jespersen etal., 1999).

The properties that make MALDI-TOF-MS a popular qualitative tool—itsability to analyze molecules across an extensive mass range, highsensitivity, minimal sample preparation and rapid analysis times—alsomake it a potentially useful quantitative tool. MALDI-TOF-MS alsoenables non-volatile and thermally labile molecules to be analyzed withrelative ease. It is therefore prudent to explore the potential ofMALDI-TOF-MS for quantitative analysis in clinical settings, fortoxicological screenings, as well as for environmental analysis. Inaddition, the application of MALDI-TOF-MS to the quantification ofpeptides and proteins is particularly relevant. The ability to quantifyintact proteins in biological tissue and fluids presents a particularchallenge in the expanding area of proteomics and investigators urgentlyrequire methods to accurately measure the absolute quantity of proteins.While there have been reports of quantitative MALDI-TOF-MS applications,there are many problems inherent to the MALDI ionization process thathave restricted its widespread use (Kazmaier et al., 1998; Horak et al.,2001; Gobom et al., 2000; Wang et al., 2000; Desiderio et al., 2000).These limitations primarily stem from factors such as the sample/matrixheterogeneity, which are believed to contribute to the large variabilityin observed signal intensities for analytes, the limited dynamic rangedue to detector saturation, and difficulties associated with couplingMALDI-TOF-MS to on-line separation techniques such as liquidchromatography. Combined, these factors are thought to compromise theaccuracy, precision, and utility with which quantitative determinationscan be made.

Because of these difficulties, practical examples of quantitativeapplications of MALDI-TOF-MS have been limited. Most of the studies todate have focused on the quantification of low mass analytes, inparticular, alkaloids or active ingredients in agricultural or foodproducts (Wang et al., 1999; Jiang et al., 2000; Wang et al., 2000; Yanget al., 2000; Wittmann et al., 2001), whereas other studies havedemonstrated the potential of MALDI-TOF-MS for the quantification ofbiologically relevant analytes such as neuropeptides, proteins,antibiotics, or various metabolites in biological tissue or fluid(Muddiman et al., 1996; Nelson et al., 1994; Duncan et al., 1993; Gobomet al., 2000; Wu et al., 1997; Mirgorodskaya et al., 2000). In earlierwork it was shown that linear calibration curves could be generated byMALDI-TOF-MS provided that an appropriate internal standard was employed(Duncan et al., 1993). This standard can “correct” for bothsample-to-sample and shot-to-shot variability. Stable isotope labeledinternal standards (isotopomers) give the best result.

With the marked improvement in resolution available on modern commercialinstruments, primarily because of delayed extraction (Bahr et al., 1997;Takach et al., 1997), the opportunity to extend quantitative work toother examples is now possible; not only of low mass analytes, but alsobiopolymers. Of particular interest is the prospect of absolutemulti-component quantification in biological samples (e.g., proteomicsapplications).

The properties of the matrix material used in the MALDI method arecritical. Only a select group of compounds is useful for the selectivedesorption of proteins and polypeptides. A review of all the matrixmaterials available for peptides and proteins shows that there arecertain characteristics the compounds must share to be analyticallyuseful. Despite its importance, very little is known about what makes amatrix material “successful” for MALDI. The few materials that do workwell are used heavily by all MALDI practitioners and new molecules areconstantly being evaluated as potential matrix candidates. With a fewexceptions, most of the matrix materials used are solid organic acids.Liquid matrices have also been investigated, but are not used routinely.

VI. Nucleic Acid Detection

In alternative embodiments for detecting protein expression, one mayassay for gene transcription. For example, an indirect method fordetecting protein expression is to detect mRNA transcripts from whichthe proteins are made. The following is a discussion of such methods,which are applicable particularly to calcyclin, calpactin I light chain,astrocytic phosphoprotein PEA-15 and tubulin-specific chaperone A in thecontext of the present invention.

1. Hybridization

There are a variety of ways by which one can assess gene expression.These methods either look at protein or at mRNA levels. Methods lookingat mRNAs all fundamentally rely, at a basic level, on nucleic acidhybridization. Hybridization is defined as the ability of a nucleic acidto selectively form duplex molecules with complementary stretches ofDNAs and/or RNAs. Depending on the application envisioned, one wouldemploy varying conditions of hybridization to achieve varying degrees ofselectivity of the probe or primers for the target sequence.

Typically, a probe or primer of between 13 and 100 nucleotides,preferably between 17 and 100 nucleotides in length up to 1-2 kilobasesor more in length will allow the formation of a duplex molecule that isboth stable and selective. Molecules having complementary sequences overcontiguous stretches greater than 20 bases in length are generallypreferred, to increase stability and selectivity of the hybrid moleculesobtained. One will generally prefer to design nucleic acid molecules forhybridization having one or more complementary sequences of 20 to 30nucleotides, or even longer where desired. Such fragments may be readilyprepared, for example, by directly synthesizing the fragment by chemicalmeans or by introducing selected sequences into recombinant vectors forrecombinant production.

For applications requiring high selectivity, one will typically desireto employ relatively high stringency conditions to form the hybrids. Forexample, relatively low salt and/or high temperature conditions, such asprovided by about 0.02 M to about 0.10 M NaCl at temperatures of about50° C. to about 70° C. Such high stringency conditions tolerate little,if any, mismatch between the probe or primers and the template or targetstrand and would be particularly suitable for isolating specific genesor for detecting specific mRNA transcripts. It is generally appreciatedthat conditions can be rendered more stringent by the addition ofincreasing amounts of formamide.

For certain applications, for example, lower stringency conditions maybe used. Under these conditions, hybridization may occur even though thesequences of the hybridizing strands are not perfectly complementary,but are mismatched at one or more positions. Conditions may be renderedless stringent by increasing salt concentration and/or decreasingtemperature. For example, a medium stringency condition could beprovided by about 0.1 to 0.25 M NaCl at temperatures of about 37° C. toabout 55° C., while a low stringency condition could be provided byabout 0.15 M to about 0.9 M salt, at temperatures ranging from about 20°C. to about 55° C. Hybridization conditions can be readily manipulateddepending on the desired results.

In other embodiments, hybridization may be achieved under conditions of,for example, 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl₂, 1.0 mMdithiothreitol, at temperatures between approximately 20° C. to about37° C. Other hybridization conditions utilized could includeapproximately 10 mM Tris-HCl (pH 8.3), 50 mM KCl, 1.5 mM MgCl₂, attemperatures ranging from approximately 40° C. to about 72° C.

In certain embodiments, it will be advantageous to employ nucleic acidsof defined sequences of the present invention in combination with anappropriate means, such as a label, for determining hybridization. Awide variety of appropriate indicator means are known in the art,including fluorescent, radioactive, enzymatic or other ligands, such asavidin/biotin, which are capable of being detected. In preferredembodiments, one may desire to employ a fluorescent label or an enzymetag such as urease, alkaline phosphatase or peroxidase, instead ofradioactive or other environmentally undesirable reagents. In the caseof enzyme tags, colorimetric indicator substrates are known that can beemployed to provide a detection means that is visibly orspectrophotometrically detectable, to identify specific hybridizationwith complementary nucleic acid containing samples.

In general, it is envisioned that the probes or primers described hereinwill be useful as reagents in solution hybridization, as in PCR™, fordetection of expression of corresponding genes, as well as inembodiments employing a solid phase. In embodiments involving a solidphase, the test DNA (or RNA) is adsorbed or otherwise affixed to aselected matrix or surface. This fixed, single-stranded nucleic acid isthen subjected to hybridization with selected probes under desiredconditions. The conditions selected will depend on the particularcircumstances (depending, for example, on the G+C content, type oftarget nucleic acid, source of nucleic acid, size of hybridizationprobe, etc.). Optimization of hybridization conditions for theparticular application of interest is well known to those of skill inthe art. After washing of the hybridized molecules to removenon-specifically bound probe molecules, hybridization is detected,and/or quantified, by determining the amount of bound label.Representative solid phase hybridization methods are disclosed in U.S.Pat. Nos. 5,843,663, 5,900,481 and 5,919,626. Other methods ofhybridization that may be used in the practice of the present inventionare disclosed in U.S. Pat. Nos. 5,849,481, 5,849,486 and 5,851,772. Therelevant portions of these and other references identified in thissection of the Specification are incorporated herein by reference.

2. Amplification of Nucleic Acids

Since many mRNAs are present in relatively low abundance, nucleic acidamplification greatly enhances the ability to assess expression. Thegeneral concept is that nucleic acids can be amplified using pairedprimers flanking the region of interest. The term “primer,” as usedherein, is meant to encompass any nucleic acid that is capable ofpriming the synthesis of a nascent nucleic acid in a template-dependentprocess. Typically, primers are oligonucleotides from ten to twentyand/or thirty base pairs in length, but longer sequences can beemployed. Primers may be provided in double-stranded and/orsingle-stranded form, although the single-stranded form is preferred.

Pairs of primers designed to selectively hybridize to nucleic acidscorresponding to selected genes are contacted with the template nucleicacid under conditions that permit selective hybridization. Dependingupon the desired application, high stringency hybridization conditionsmay be selected that will only allow hybridization to sequences that arecompletely complementary to the primers. In other embodiments,hybridization may occur under reduced stringency to allow foramplification of nucleic acids contain one or more mismatches with theprimer sequences. Once hybridized, the template-primer complex iscontacted with one or more enzymes that facilitate template-dependentnucleic acid synthesis. Multiple rounds of amplification, also referredto as “cycles,” are conducted until a sufficient amount of amplificationproduct is produced.

The amplification product may be detected or quantified. In certainapplications, the detection may be performed by visual means.Alternatively, the detection may involve indirect identification of theproduct via chemilluminescence, radioactive scintigraphy of incorporatedradiolabel or fluorescent label or even via a system using electricaland/or thermal impulse signals.

A number of template dependent processes are available to amplify theoligonucleotide sequences present in a given template sample. One of thebest known amplification methods is the polymerase chain reaction(referred to as PCR™) which is described in detail in U.S. Pat. Nos.4,683,195, 4,683,202 and 4,800,159, and in Innis et al., 1988, each ofwhich is incorporated herein by reference in their entirety.

A reverse transcriptase PCR™ amplification procedure may be performed toquantify the amount of mRNA amplified. Methods of reverse transcribingRNA into cDNA are well known (see Sambrook et al., 1989). Alternativemethods for reverse transcription utilize thermostable DNA polymerases.These methods are described in WO 90/07641. Polymerase chain reactionmethodologies are well known in the art. Representative methods ofRT-PCR are described in U.S. Pat. No. 5,882,864.

Whereas standard PCR usually uses one pair of primers to amplify aspecific sequence, multiplex-PCR (MPCR) uses multiple pairs of primersto amplify many sequences simultaneously (Chamberlan et al., 1990). Thepresence of many PCR primers in a single tube could cause many problems,such as the increased formation of misprimed PCR products and “primerdimers”, the amplification discrimination of longer DNA fragment and soon. Normally, MPCR buffers contain a Taq Polymerase additive, whichdecreases the competition among amplicons and the amplificationdiscrimination of longer DNA fragment during MPCR. MPCR products canfurther be hybridized with gene-specific probe for verification.Theoretically, one should be able to use as many as primers asnecessary. However, due to side effects (primer dimers, misprimed PCRproducts, etc.) caused during MPCR, there is a limit (less than 20) tothe number of primers that can be used in a MPCR reaction. See alsoEuropean Application No. 0 364 255 and Mueller and Wold (1989).

Another method for amplification is ligase chain reaction (“LCR”),disclosed in European Application No. 320 308, incorporated herein byreference in its entirety. U.S. Pat. No. 4,883,750 describes a methodsimilar to LCR for binding probe pairs to a target sequence. A methodbased on PCR™ and oligonucleotide ligase assay (OLA), disclosed in U.S.Pat. No. 5,912,148, may also be used.

Alternative methods for amplification of target nucleic acid sequencesthat may be used in the practice of the present invention are disclosedin U.S. Pat. Nos. 5,843,650, 5,846,709, 5,846,783, 5,849,546, 5,849,497,5,849,547, 5,858,652, 5,866,366, 5,916,776, 5,922,574, 5,928,905,5,928,906, 5,932,451, 5,935,825, 5,939,291 and 5,942,391, GB ApplicationNo. 2 202 328, and in PCT Application No. PCT/US89/01025, each of whichis incorporated herein by reference in its entirety.

Qbeta Replicase, described in PCT Application No. PCT/US87/00880, mayalso be used as an amplification method in the present invention. Inthis method, a replicative sequence of RNA that has a regioncomplementary to that of a target is added to a sample in the presenceof an RNA polymerase. The polymerase will copy the replicative sequencewhich may then be detected.

An isothermal amplification method, in which restriction endonucleasesand ligases are used to achieve the amplification of target moleculesthat contain nucleotide 5′-[alpha-thio]-triphosphates in one strand of arestriction site may also be useful in the amplification of nucleicacids in the present invention (Walker et al., 1992). StrandDisplacement Amplification (SDA), disclosed in U.S. Pat. No. 5,916,779,is another method of carrying out isothermal amplification of nucleicacids which involves multiple rounds of strand displacement andsynthesis, i.e., nick translation.

Other nucleic acid amplification procedures include transcription-basedamplification systems (TAS), including nucleic acid sequence basedamplification (NASBA) and 3SR (Kwoh et al., 1989; Gingeras et al., PCTApplication WO 88/10315, incorporated herein by reference in theirentirety). European Application No. 329 822 disclose a nucleic acidamplification process involving cyclically synthesizing single-strandedRNA (“ssRNA”), ssDNA, and double-stranded DNA (dsDNA), which may be usedin accordance with the present invention.

PCT Application WO 89/06700 (incorporated herein by reference in itsentirety) disclose a nucleic acid sequence amplification scheme based onthe hybridization of a promoter region/primer sequence to a targetsingle-stranded DNA (“ssDNA”) followed by transcription of many RNAcopies of the sequence. This scheme is not cyclic, i.e., new templatesare not produced from the resultant RNA transcripts. Other amplificationmethods include “race” and “one-sided PCR” (Frohman, 1990; Ohara et al.,1989).

3. Detection of Nucleic Acids

Following any amplification, it may be desirable to separate theamplification product from the template and/or the excess primer. In oneembodiment, amplification products are separated by agarose,agarose-acrylamide or polyacrylamide gel electrophoresis using standardmethods (Sambrook et al., 1989). Separated amplification products may becut out and eluted from the gel for further manipulation. Using lowmelting point agarose gels, the separated band may be removed by heatingthe gel, followed by extraction of the nucleic acid.

Separation of nucleic acids may also be effected by chromatographictechniques known in art. There are many kinds of chromatography whichmay be used in the practice of the present invention, includingadsorption, partition, ion-exchange, hydroxylapatite, molecular sieve,reverse-phase, column, paper, thin-layer, and gas chromatography as wellas HPLC.

In certain embodiments, the amplification products are visualized. Atypical visualization method involves staining of a gel with ethidiumbromide and visualization of bands under UV light. Alternatively, if theamplification products are integrally labeled with radio- orfluorometrically-labeled nucleotides, the separated amplificationproducts can be exposed to x-ray film or visualized under theappropriate excitatory spectra.

In one embodiment, following separation of amplification products, alabeled nucleic acid probe is brought into contact with the amplifiedmarker sequence. The probe preferably is conjugated to a chromophore butmay be radiolabeled. In another embodiment, the probe is conjugated to abinding partner, such as an antibody or biotin, or another bindingpartner carrying a detectable moiety.

In particular embodiments, detection is by Southern blotting andhybridization with a labeled probe. The techniques involved in Southernblotting are well known to those of skill in the art (see Sambrook etal., 1989). One example of the foregoing is described in U.S. Pat. No.5,279,721, incorporated by reference herein, which discloses anapparatus and method for the automated electrophoresis and transfer ofnucleic acids. The apparatus permits electrophoresis and blottingwithout external manipulation of the gel and is ideally suited tocarrying out methods according to the present invention.

Other methods of nucleic acid detection that may be used in the practiceof the instant invention are disclosed in U.S. Pat. Nos. 5,840,873,5,843,640, 5,843,651, 5,846,708, 5,846,717, 5,846,726, 5,846,729,5,849,487, 5,853,990, 5,853,992, 5,853,993, 5,856,092, 5,861,244,5,863,732, 5,863,753, 5,866,331, 5,905,024, 5,910,407, 5,912,124,5,912,145, 5,919,630, 5,925,517, 5,928,862, 5,928,869, 5,929,227,5,932,413 and 5,935,791, each of which is incorporated herein byreference.

4. Nucleic Acid Arrays

Microarrays comprise a plurality of polymeric molecules spatiallydistributed over, and stably associated with, the surface of asubstantially planar substrate, e.g., biochips. Microarrays ofpolynucleotides have been developed and find use in a variety ofapplications, such as screening and DNA sequencing. One area inparticular in which microarrays find use is in gene expression analysis.

In gene expression analysis with microarrays, an array of “probe”oligonucleotides is contacted with a nucleic acid sample of interest,i.e., target, such as polyA mRNA from a particular tissue type. Contactis carried out under hybridization conditions and unbound nucleic acidis then removed. The resultant pattern of hybridized nucleic acidprovides information regarding the genetic profile of the sample tested.Methodologies of gene expression analysis on microarrays are capable ofproviding both qualitative and quantitative information.

A variety of different arrays which may be used are known in the art.The probe molecules of the arrays which are capable of sequence specifichybridization with target nucleic acid may be polynucleotides orhybridizing analogues or mimetics thereof, including: nucleic acids inwhich the phosphodiester linkage has been replaced with a substitutelinkage, such as phosphorothioate, methylimino, methylphosphonate,phosphoramidate, guanidine and the like; nucleic acids in which theribose subunit has been substituted, e.g., hexose phosphodiester;peptide nucleic acids; and the like. The length of the probes willgenerally range from 10 to 1000 nts, where in some embodiments theprobes will be oligonucleotides and usually range from 15 to 150 nts andmore usually from 15 to 100 nts in length, and in other embodiments theprobes will be longer, usually ranging in length from 150 to 1000 nts,where the polynucleotide probes may be single- or double-stranded,usually single-stranded, and may be PCR fragments amplified from cDNA.

The probe molecules on the surface of the substrates will correspond toselected genes being analyzed and be positioned on the array at a knownlocation so that positive hybridization events may be correlated toexpression of a particular gene in the physiological source from whichthe target nucleic acid sample is derived. The substrates with which theprobe molecules are stably associated may be fabricated from a varietyof materials, including plastics, ceramics, metals, gels, membranes,glasses, and the like. The arrays may be produced according to anyconvenient methodology, such as preforming the probes and then stablyassociating them with the surface of the support or growing the probesdirectly on the support. A number of different array configurations andmethods for their production are known to those of skill in the art anddisclosed in U.S. Pat. Nos. 5,445,934, 5,532,128, 5,556,752, 5,242,974,5,384,261, 5,405,783, 5,412,087, 5,424,186, 5,429,807, 5,436,327,5,472,672, 5,527,681, 5,529,756, 5,545,531, 5,554,501, 5,561,071,5,571,639, 5,593,839, 5,599,695, 5,624,711, 5,658,734, 5,700,637, and6,004,755.

Following hybridization, where non-hybridized labeled nucleic acid iscapable of emitting a signal during the detection step, a washing stepis employed where unhybridized labeled nucleic acid is removed from thesupport surface, generating a pattern of hybridized nucleic acid on thesubstrate surface. A variety of wash solutions and protocols for theiruse are known to those of skill in the art and may be used.

Where the label on the target nucleic acid is not directly detectable,one then contacts the array, now comprising bound target, with the othermember(s) of the signal producing system that is being employed. Forexample, where the label on the target is biotin, one then contacts thearray with streptavidin-fluorescer conjugate under conditions sufficientfor binding between the specific binding member pairs to occur.Following contact, any unbound members of the signal producing systemwill then be removed, e.g., by washing. The specific wash conditionsemployed will necessarily depend on the specific nature of the signalproducing system that is employed, and will be known to those of skillin the art familiar with the particular signal producing systememployed.

The resultant hybridization pattern(s) of labeled nucleic acids may bevisualized or detected in a variety of ways, with the particular mannerof detection being chosen based on the particular label of the nucleicacid, where representative detection means include scintillationcounting, autoradiography, fluorescence measurement, calorimetricmeasurement, light emission measurement and the like.

Prior to detection or visualization, where one desires to reduce thepotential for a mismatch hybridization event to generate a falsepositive signal on the pattern, the array of hybridized target/probecomplexes may be treated with an endonuclease under conditionssufficient such that the endonuclease degrades single stranded, but notdouble stranded DNA. A variety of different endonucleases are known andmay be used, where such nucleases include: mung bean nuclease, S1nuclease, and the like. Where such treatment is employed in an assay inwhich the target nucleic acids are not labeled with a directlydetectable label, e.g., in an assay with biotinylated target nucleicacids, the endonuclease treatment will generally be performed prior tocontact of the array with the other member(s) of the signal producingsystem, e.g., fluorescent-streptavidin conjugate. Endonucleasetreatment, as described above, ensures that only end-labeledtarget/probe complexes having a substantially complete hybridization atthe 3′ end of the probe are detected in the hybridization pattern.

Following hybridization and any washing step(s) and/or subsequenttreatments, as described above, the resultant hybridization pattern isdetected. In detecting or visualizing the hybridization pattern, theintensity or signal value of the label will be not only be detected butquantified, by which is meant that the signal from each spot of thehybridization will be measured and compared to a unit valuecorresponding the signal emitted by known number of end-labeled targetnucleic acids to obtain a count or absolute value of the copy number ofeach end-labeled target that is hybridized to a particular spot on thearray in the hybridization pattern.

VI. Gene Therapy

In another embodiment, the present invention provides for theadministration of a gene therapy vector encoding one or more genesidentified as being downregulated in gliomas. Alternatively, for genesthat are overexpressed in gliomas, the transgenes may provide forreduced expression of appropriate targets. Various aspects of genedelivery and expression are set forth below.

1. Therapeutic Transgenes

Thus, in accordance with the present invention, there are providedmethods of treating cancer utilizing genes identified as beingoverexpressed or underexpressed in gliomas. By inhibiting or increasingthe expression of various of these genes, therapeutic benefit may beprovided to patients.

2. Antisense

The term “antisense” nucleic acid refers to oligo- and polynucleotidescomplementary to bases sequences of a target DNA or RNA. When introducedinto a cell, antisense molecules hybridize to a target nucleic acid andinterfere with its transcription, transport, processing, splicing ortranslation. Targeting double-stranded DNA leads to triple helixformation; targeting RNA will lead to double helix formation.

Antisense constructs may be designed to bind to the promoter or othercontrol regions, exons, introns or even exon-intron boundaries of agene. Antisense RNA constructs, or DNA encoding such antisense RNA's,may be employed to inhibit gene transcription or translation within ahost cell. Nucleic acid sequences which comprise “complementarynucleotides” are those which are capable of base-pairing according tothe standard Watson-Crick complementarity rules. That is, that thelarger purines will base pair with the smaller pyrimidines to formcombinations of guanine paired with cytosine (G:C) and adenine pairedwith either thymine in the case of DNA (A:T), or uracil (A:U) in thecase of RNA. Inclusion of less common bases such as inosine,5-methylcytosine, 6-methyladenine, hypoxanthine and others inhybridizing sequences does not interfere with pairing.

As used herein, the terms “complementary” and “antisense sequences” meannucleic acid sequences that are substantially complementary over theirentire length and have very few base mismatches. For example, nucleicacid sequences of fifteen bases in length may be termed complementarywhen they have complementary nucleotides at thirteen or fourteenpositions. Naturally, nucleic acid sequences with are “completelycomplementary” will be nucleic acid sequences which have perfect basepair matching with the target sequences, i.e., no mismatches. Othersequences with lower degrees of homology are contemplated. For example,an antisense construct with limited regions of high homology, butoverall containing a lower degree (50% or less) total homology, may beused.

While all or part of the gene sequence may be employed in the context ofantisense construction, statistically, any sequence of 17 bases longshould occur only once in the human genome and, therefore, suffice tospecify a unique target. Although shorter oligomers are easier to makeand increase in vivo accessibility, numerous other factors are involvedin determining the specificity of hybridization. Both binding affinityand sequence specificity of an oligonucleotide to its complementarytarget increases with increasing length. It is contemplated thatoligonucleotides of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 ormore base pairs will be used. One can readily determine whether a givenantisense nucleic acid is effective at targeting a gene simply bytesting the construct in vitro to determine whether the gene's functionor expression is affected.

In certain embodiments, one may wish to employ antisense constructswhich include other elements, for example, those which include C-5propyne pyrimidines. Oligonucleotides which contain C-5 propyne analogsof uridine and cytidine have been shown to bind RNA with high affinityand to be potent inhibitors or gene expression. Wagner et al. (1993).

3. Ribozymes

The term “ribozyme” refers to an RNA-based enzyme capable of targetingand cleaving particular DNA and RNA sequences. Ribozymes can either betargeted directly to cells, in the form of RNA oligonucleotidesincorporating ribozyme sequences, or introduced into the cell as anexpression construct encoding the desired ribozymal RNA. Ribozymes maybe used and applied in much the same way as described for antisensenucleic acids. Ribozyme sequences also may be modified in much the sameway as described for antisense nucleic acids. For example, one couldinclude modified bases or modified phosphate backbones to improvestability or function.

4. Single Chain Antibodies

Naturally-occurring antibodies (of isotype IgG) produced by B cells,consist of four polypeptide chains. Two heavy chains (composed of fourimmunoglobulin domains) and two light chains (made up of twoimmunoglobulin domains) are held together by disulphide bonds. The bulkof the antibody complex is made up of constant immunoglobulin domains.These have a conserved amino acid sequence, and exhibit low variability.Different classes of constant regions in the stem of the antibodygenerate different isotypes of antibody with differing properties. Therecognition properties of the antibody are carried by the variableregions (VH and VL) at the ends of the arms. Each variable domaincontains three hypervariable regions known as complementaritydetermining regions, or CDRs. The CDRs come together in the finaltertiary structure to form an antigen binding pocket. The human genomecontains multiple fragments encoding portions of the variable domains inregions of the immunoglobulin gene cluster known as V, D and J. During Bcell development these regions undergo recombination to generate a broaddiversity of antibody affinities. As these B cell populations mature inthe presence of a target antigen, hypermutation of the variable regiontakes place, with the B cells producing the most active antibodies beingselected for further expansion in a process known as affinitymaturation.

A major breakthrough was the generation of monoclonal antibodies, purepopulations of antibodies with the same affinity. This was achieved byfusing B cells taken from immunized animals with myeloma cells. Thisgenerates a population of immortal hybridomas, from which the requiredclones can be selected. Monoclonal antibodies are very importantresearch tools, and have been used in some therapies. However, they arevery expensive and difficult to produce, and if used in a therapeuticcontext, can elicit and immune response which will destroy the antibody.This can be reduced in part by humanizing the antibody by grafting theCDRs from the parent monoclonal into the backbone of a human IgGantibody. It may be better to deliver antibodies by gene therapy, asthis would hopefully provide a constant localized supply of antibodyfollowing a single dose of vector. The problems of vector design anddelivery are dealt with elsewhere, but antibodies in their native form,consisting of two different polypeptide chains which need to begenerated in approximately equal amounts and assembled correctly are notgood candidates for gene therapy. However, it is possible to create asingle polypeptide which can retain the antigen binding properties of amonoclonal antibody.

The variable regions from the heavy and light chains (VH and VL) areboth approximately 110 amino acids long. They can be linked by a 15amino acid linker (e.g., (glycine₄serine)₃), which has sufficientflexibility to allow the two domains to assemble a functional antigenbinding pocket. Addition of various signal sequences allows the scFv tobe targeted to different organelles within the cell, or to be secreted.Addition of the light chain constant region (Ck) allows dimerization viadisulphide bonds, giving increased stability and avidity. However, thereis evidence that scFvs spontaneously multimerize, with the extent ofaggregation (presumably via exposed hydrophobic surfaces) beingdependent on the length of the glycine-serine linker.

The variable regions for constructing the scFv are obtained as follows.Using a monoclonal antibody against the target of interest, it is asimple procedure to use RT-PCR to clone out the variable regions frommRNA extracted from the parent hybridoma. Degenerate primers targeted tothe relatively invariant framework regions can be used. Expressionconstructs are available with convenient cloning sites for the insertionof the cloned variable regions.

5. siRNA

RNA interference (also referred to as “RNA-mediated interference” orRNAi) is a mechanism by which gene expression can be reduced oreliminated. Double-stranded RNA (dsRNA) has been observed to mediate thereduction, which is a multi-step process. dsRNA activatespost-transcriptional gene expression surveillance mechanisms that appearto function to defend cells from virus infection and transposon activity(Fire et al., 1998; Grishok et al., 2000; Ketting et al., 1999; Lin andAvery et al., 1999; Montgomery et al., 1998; Sharp and Zamore, 2000;Tabara et al., 1999). Activation of these mechanisms targets mature,dsRNA-complementary mRNA for destruction. RNAi offers major experimentaladvantages for study of gene function. These advantages include a veryhigh specificity, ease of movement across cell membranes, and prolongeddown-regulation of the targeted gene (Fire et al., 1998; Grishok et al.,2000; Ketting et al., 1999; Lin and Avery et al., 1999; Montgomery etal., 1998; Sharp et al., 1999; Sharp and Zamore, 2000; Tabara et al.,1999). Moreover, dsRNA has been shown to silence genes in a wide rangeof systems, including plants, protozoans, fungi, C. elegans,Trypanasoma, Drosophila, and mammals (Grishok et al., 2000; Sharp etal., 1999; Sharp and Zamore, 2000; Elbashir et al., 2001). It isgenerally accepted that RNAi acts post-transcriptionally, targeting RNAtranscripts for degradation. It appears that both nuclear andcytoplasmic RNA can be targeted (Bosher and Labouesse, 2000).

siRNAs must be designed so that they are specific and effective insuppressing the expression of the genes of interest. Methods ofselecting the target sequences, i.e., those sequences present in thegene or genes of interest to which the siRNAs will guide the degradativemachinery, are directed to avoiding sequences that may interfere withthe siRNA's guide function while including sequences that are specificto the gene or genes. Typically, siRNA target sequences of about 21 to23 nucleotides in length are most effective. This length reflects thelengths of digestion products resulting from the processing of muchlonger RNAs as described above (Montgomery et al., 1998).

The making of siRNAs has been mainly through direct chemical synthesis;through processing of longer, double-stranded RNAs through exposure toDrosophila embryo lysates; or through an in vitro system derived from S2cells. Use of cell lysates or in vitro processing may further involvethe subsequent isolation of the short, 21-23 nucleotide siRNAs from thelysate, etc., making the process somewhat cumbersome and expensive.Chemical synthesis proceeds by making two single-stranded RNA-oligomersfollowed by the annealing of the two single-stranded oligomers into adouble-stranded RNA. Methods of chemical synthesis are diverse.Non-limiting examples are provided in U.S. Pat. Nos. 5,889,136,4,415,723, and 4,458,066, expressly incorporated herein by reference,and in Wincott et al. (1995).

Several further modifications to siRNA sequences have been suggested inorder to alter their stability or improve their effectiveness. It issuggested that synthetic complementary 21-mer RNAs having di-nucleotideoverhangs (i.e., 19 complementary nucleotides+3′ non-complementarydimers) may provide the greatest level of suppression. These protocolsprimarily use a sequence of two (2′-deoxy) thymidine nucleotides as thedi-nucleotide overhangs. These dinucleotide overhangs are often writtenas dTdT to distinguish them from the typical nucleotides incorporatedinto RNA. The literature has indicated that the use of dT overhangs isprimarily motivated by the need to reduce the cost of the chemicallysynthesized RNAs. It is also suggested that the dTdT overhangs might bemore stable than UU overhangs, though the data available shows only aslight (<20%) improvement of the dTdT overhang compared to an siRNA witha UU overhang.

Chemically synthesized siRNAs are found to work optimally when they arein cell culture at concentrations of 25-100 nM, but concentrations ofabout 100 nM have achieved effective suppression of expression inmammalian cells. siRNAs have been most effective in mammalian cellculture at about 100 nM. In several instances, however, lowerconcentrations of chemically synthesized siRNA have been used (Caplen,et al., 2000; Elbashir et al., 2001).

WO 99/32619 and WO 01/68836 suggest that RNA for use in siRNA may bechemically or enzymatically synthesized. Both of these texts areincorporated herein in their entirety by reference. The enzymaticsynthesis contemplated in these references is by a cellular RNApolymerase or a bacteriophage RNA polymerase (e.g., T3, T7, SP6) via theuse and production of an expression construct as is known in the art.For example, see U.S. Pat. No. 5,795,715. The contemplated constructsprovide templates that produce RNAs that contain nucleotide sequencesidentical to a portion of the target gene. The length of identicalsequences provided by these references is at least 25 bases, and may beas many as 400 or more bases in length. An important aspect of thisreference is that the authors contemplate digesting longer dsRNAs to21-25mer lengths with the endogenous nuclease complex that converts longdsRNAs to siRNAs in vivo. They do not describe or present data forsynthesizing and using in vitro transcribed 21-25mer dsRNAs. Nodistinction is made between the expected properties of chemical orenzymatically synthesized dsRNA in its use in RNA interference.

Similarly, WO 00/44914, incorporated herein by reference, suggests thatsingle strands of RNA can be produced enzymatically or by partial/totalorganic synthesis. Preferably, single-stranded RNA is enzymaticallysynthesized from the PCR products of a DNA template, preferably a clonedcDNA template and the RNA product is a complete transcript of the cDNA,which may comprise hundreds of nucleotides. WO 01/36646, incorporatedherein by reference, places no limitation upon the manner in which thesiRNA is synthesized, providing that the RNA may be synthesized in vitroor in vivo, using manual and/or automated procedures. This referencealso provides that in vitro synthesis may be chemical or enzymatic, forexample using cloned RNA polymerase (e.g., T3, T7, SP6) fortranscription of the endogenous DNA (or cDNA) template, or a mixture ofboth. Again, no distinction in the desirable properties for use in RNAinterference is made between chemically or enzymatically synthesizedsiRNA.

U.S. Pat. No. 5,795,715 reports the simultaneous transcription of twocomplementary DNA sequence strands in a single reaction mixture, whereinthe two transcripts are immediately hybridized. The templates used arepreferably of between 40 and 100 base pairs, and which is equipped ateach end with a promoter sequence. The templates are preferably attachedto a solid surface. After transcription with RNA polymerase, theresulting dsRNA fragments may be used for detecting and/or assayingnucleic acid target sequences.

6. Vectors

In accordance with the present invention, both stimulatory andinhibitory genes may be provided to a cancer cell and expressed therein.Stimulatory genes are generally simply copies of the gene of interest,although in some cases they may be genes, the expression of which directthe expression of the gene of interest. Inhibitory genes, discussedabove, may include expression constructs for antisense molecules,ribozymes, interfering RNAs or single-chain antibodies.

The term “vector” is used to refer to a carrier nucleic acid moleculeinto which a nucleic acid sequence can be inserted for introduction intoa cell where it can be replicated. A nucleic acid sequence can be“exogenous,” which means that it is foreign to the cell into which thevector is being introduced or that the sequence is homologous to asequence in the cell but in a position within the host cell nucleic acidin which the sequence is ordinarily not found. Vectors include plasmids,cosmids, viruses (bacteriophage, animal viruses, and plant viruses), andartificial chromosomes (e.g., YACs). One of skill in the art would bewell equipped to construct a vector through standard recombinanttechniques (see, for example, Maniatis et al., 1989 and Ausubel et al.,1994, both incorporated herein by reference).

The term “expression vector” refers to any type of genetic constructcomprising a nucleic acid coding for a RNA capable of being transcribed.In some cases, RNA molecules are then translated into a protein,polypeptide, or peptide. In other cases, these sequences are nottranslated, for example, in the production of antisense molecules orribozymes. Expression vectors can contain a variety of “controlsequences,” which refer to nucleic acid sequences necessary for thetranscription and possibly translation of an operably linked codingsequence in a particular host cell. In addition to control sequencesthat govern transcription and translation, vectors and expressionvectors may contain nucleic acid sequences that serve other functions aswell and are described infra.

a. Promoters and Enhancers

A “promoter” is a control sequence that is a region of a nucleic acidsequence at which initiation and rate of transcription are controlled.It may contain genetic elements at which regulatory proteins andmolecules may bind, such as RNA polymerase and other transcriptionfactors, to initiate the specific transcription a nucleic acid sequence.The phrases “operatively positioned,” “operatively linked,” “undercontrol,” and “under transcriptional control” mean that a promoter is ina correct functional location and/or orientation in relation to anucleic acid sequence to control transcriptional initiation and/orexpression of that sequence.

A promoter generally comprises a sequence that functions to position thestart site for RNA synthesis. The best known example of this is the TATAbox, but in some promoters lacking a TATA box, such as, for example, thepromoter for the mammalian terminal deoxynucleotidyl transferase geneand the promoter for the SV40 late genes, a discrete element overlyingthe start site itself helps to fix the place of initiation. Additionalpromoter elements regulate the frequency of transcriptional initiation.Typically, these are located in the region 30-110 bp upstream of thestart site, although a number of promoters have been shown to containfunctional elements downstream of the start site as well. To bring acoding sequence “under the control of” a promoter, one positions the 5′end of the transcription initiation site of the transcriptional readingframe “downstream” of (i.e., 3′ of) the chosen promoter. The “upstream”promoter stimulates transcription of the DNA and promotes expression ofthe encoded RNA.

The spacing between promoter elements frequently is flexible, so thatpromoter function is preserved when elements are inverted or movedrelative to one another. In the tk promoter, the spacing betweenpromoter elements can be increased to 50 bp apart before activity beginsto decline. Depending on the promoter, it appears that individualelements can function either cooperatively or independently to activatetranscription. A promoter may or may not be used in conjunction with an“enhancer,” which refers to a cis-acting regulatory sequence involved inthe transcriptional activation of a nucleic acid sequence.

A promoter may be one naturally associated with a nucleic acid sequence,as may be obtained by isolating the 5′ non-coding sequences locatedupstream of the coding segment and/or exon. Such a promoter can bereferred to as “endogenous.” Similarly, an enhancer may be one naturallyassociated with a nucleic acid sequence, located either downstream orupstream of that sequence. Alternatively, certain advantages will begained by positioning the coding nucleic acid segment under the controlof a recombinant or heterologous promoter, which refers to a promoterthat is not normally associated with a nucleic acid sequence in itsnatural environment. A recombinant or heterologous enhancer refers alsoto an enhancer not normally associated with a nucleic acid sequence inits natural environment. Such promoters or enhancers may includepromoters or enhancers of other genes, and promoters or enhancersisolated from any other virus, or prokaryotic or eukaryotic cell, andpromoters or enhancers not “naturally occurring,” i.e., containingdifferent elements of different transcriptional regulatory regions,and/or mutations that alter expression. For example, promoters that aremost commonly used in recombinant DNA construction include theβ-lactamase (penicillinase), lactose and tryptophan (trp) promotersystems. In addition to producing nucleic acid sequences of promotersand enhancers synthetically, sequences may be produced using recombinantcloning and/or nucleic acid amplification technology, including PCR™, inconnection with the compositions disclosed herein (see U.S. Pat. Nos.4,683,202 and 5,928,906, each incorporated herein by reference).Furthermore, it is contemplated the control sequences that directtranscription and/or expression of sequences within non-nuclearorganelles such as mitochondria, chloroplasts, and the like, can beemployed as well.

Naturally, it will be important to employ a promoter and/or enhancerthat effectively directs the expression of the DNA segment in theorganelle, cell type, tissue, organ, or organism chosen for expression.Those of skill in the art of molecular biology generally know the use ofpromoters, enhancers, and cell type combinations for protein expression,(see, for example Sambrook et al. 1989, incorporated herein byreference). The promoters employed may be constitutive, tissue-specific,inducible, and/or useful under the appropriate conditions to direct highlevel expression of the introduced DNA segment, such as is advantageousin the large-scale production of recombinant proteins and/or peptides.The promoter may be heterologous or endogenous.

Additionally any promoter/enhancer combination (as per, for example, theEukaryotic Promoter Data Base EPDB, http://www.epd.isb-sib.ch/) couldalso be used to drive expression. Use of a T3, T7 or SP6 cytoplasmicexpression system is another possible embodiment. Eukaryotic cells cansupport cytoplasmic transcription from certain bacterial promoters ifthe appropriate bacterial polymerase is provided, either as part of thedelivery complex or as an additional genetic expression construct.

Table 1 lists non-limiting examples of elements/promoters that may beemployed, in the context of the present invention, to regulate theexpression of a RNA. Table 2 provides non-limiting examples of inducibleelements, which are regions of a nucleic acid sequence that can beactivated in response to a specific stimulus.

TABLE 1 Promoter and/or Enhancer Promoter/Enhancer ReferencesImmunoglobulin Heavy Chain Banerji et al., 1983; Gilles et al., 1983;Grosschedl et al., 1985; Atchinson et al., 1986, 1987; Imler et al.,1987; Weinberger et al., 1984; Kiledjian et al., 1988; Porton et al.;1990 Immunoglobulin Light Chain Queen et al., 1983; Picard et al., 1984T-Cell Receptor Luria et al., 1987; Winoto et al., 1989; Redondo et al.;1990 HLA DQ a and/or DQ β Sullivan et al., 1987 β-Interferon Goodbournet al., 1986; Fujita et al., 1987; Goodbourn et al., 1988 Interleukin-2Greene et al., 1989 Interleukin-2 Receptor Greene et al., 1989; Lin etal., 1990 MHC Class II 5 Koch et al., 1989 MHC Class II HLA-Dra Shermanet al., 1989 β-Actin Kawamoto et al., 1988; Ng et al.; 1989 MuscleCreatine Kinase (MCK) Jaynes et al., 1988; Horlick et al., 1989; Johnsonet al., 1989 Prealbumin (Transthyretin) Costa et al., 1988 Elastase IOrnitz et al., 1987 Metallothionein (MTII) Karin et al., 1987; Culottaet al., 1989 Collagenase Pinkert et al., 1987; Angel et al., 1987Albumin Pinkert et al., 1987; Tronche et al., 1989, 1990 α-FetoproteinGodbout et al., 1988; Campere et al., 1989 γ-Globin Bodine et al., 1987;Perez-Stable et al., 1990 β-Globin Trudel et al., 1987 c-fos Cohen etal., 1987 c-HA-ras Triesman, 1986; Deschamps et al., 1985 Insulin Edlundet al., 1985 Neural Cell Adhesion Molecule Hirsch et al., 1990 (NCAM)α₁-Antitrypsin Latimer et al., 1990 H2B (TH2B) Histone Hwang et al.,1990 Mouse and/or Type I Collagen Ripe et al., 1989 Glucose-RegulatedProteins Chang et al., 1989 (GRP94 and GRP78) Rat Growth Hormone Larsenet al., 1986 Human Serum Amyloid A (SAA) Edbrooke et al., 1989 TroponinI (TN I) Yutzey et al., 1989 Platelet-Derived Growth Factor Pech et al.,1989 (PDGF) Duchenne Muscular Dystrophy Klamut et al., 1990 SV40 Banerjiet al., 1981; Moreau et al., 1981; Sleigh et al., 1985; Firak et al.,1986; Herr et al., 1986; Imbra et al., 1986; Kadesch et al., 1986; Wanget al., 1986; Ondek et al., 1987; Kuhl et al., 1987; Schaffner et al.,1988 Polyoma Swartzendruber et al., 1975; Vasseur et al., 1980; Katinkaet al., 1980, 1981; Tyndell et al., 1981; Dandolo et al., 1983; deVilliers et al., 1984; Hen et al., 1986; Satake et al., 1988; Campbelland/or Villarreal, 1988 Retroviruses Kriegler et al., 1982, 1983;Levinson et al., 1982; Kriegler et al., 1983, 1984a, b, 1988; Bosze etal., 1986; Miksicek et al., 1986; Celander et al., 1987; Thiesen et al.,1988; Celander et al., 1988; Choi et al., 1988; Reisman et al., 1989Papilloma Virus Campo et al., 1983; Lusky et al., 1983; Spandidos and/orWilkie, 1983; Spalholz et al., 1985; Lusky et al., 1986; Cripe et al.,1987; Gloss et al., 1987; Hirochika et al., 1987; Stephens et al., 1987Hepatitis B Virus Bulla et al., 1986; Jameel et al., 1986; Shaul et al.,1987; Spandau et al., 1988; Vannice et al., 1988 Human ImmunodeficiencyVirus Muesing et al., 1987; Hauber et al., 1988; Jakobovits et al.,1988; Feng et al., 1988; Takebe et al., 1988; Rosen et al., 1988;Berkhout et al., 1989; Laspia et al., 1989; Sharp et al., 1989; Braddocket al., 1989 Cytomegalovirus (CMV) Weber et al., 1984; Boshart et al.,1985; Foecking et al., 1986 Gibbon Ape Leukemia Virus Holbrook et al.,1987; Quinn et al., 1989

TABLE 2 Inducible Elements Element Inducer References MT II PhorbolEster (TFA) Palmiter et al., 1982; Haslinger Heavy metals et al., 1985;Searle et al., 1985; Stuart et al., 1985; Imagawa et al., 1987, Karin etal., 1987; Angel et al., 1987b; McNeall et al., 1989 MMTV (mouse mammaryGlucocorticoids Huang et al., 1981; Lee et al., tumor virus) 1981;Majors et al., 1983; Chandler et al., 1983; Lee et al., 1984; Ponta etal., 1985; Sakai et al., 1988 β-Interferon Poly(rI) × Tavernier et al.,1983 Poly(rc) Adenovirus 5 E2 ElA Imperiale et al., 1984 CollagenasePhorbol Ester (TPA) Angel et al., 1987a Stromelysin Phorbol Ester (TPA)Angel et al., 1987b SV40 Phorbol Ester (TPA) Angel et al., 1987b MurineMX Gene Interferon, Newcastle Hug et al., 1988 Disease Virus GRP78 GeneA23187 Resendez et al., 1988 α-2-Macroglobulin IL-6 Kunz et al., 1989Vimentin Serum Rittling et al., 1989 MHC Class I Gene H-2κb InterferonBlanar et al., 1989 HSP70 ElA, SV40 Large T Taylor et al., 1989, 1990a,1990b Antigen Proliferin Phorbol Ester-TPA Mordacq et al., 1989 TumorNecrosis Factor α PMA Hensel et al., 1989 Thyroid Stimulating ThyroidHormone Chatterjee et al., 1989 Hormone α Gene

The identity of tissue-specific promoters or elements, as well as assaysto characterize their activity, is well known to those of skill in theart. Non-limiting examples of such regions include the human LIMK2 gene(Nomoto et al., 1999), the somatostatin receptor 2 gene (Kraus et al.,1998), murine epididymal retinoic acid-binding gene (Lareyre et al.,1999), human CD4 (Zhao-Emonet et al., 1998), mouse alpha2 (XI) collagen(Tsumaki et al., 1998), DIA dopamine receptor gene (Lee et al., 1997),insulin-like growth factor II (Wu et al., 1997), and human plateletendothelial cell adhesion molecule-1 (Almendro et al., 1996).

b. Initiation Signals and Internal Ribosome Binding Sites

A specific initiation signal also may be required for efficienttranslation of coding sequences. These signals include the ATGinitiation codon or adjacent sequences. Exogenous translational controlsignals, including the ATG initiation codon, may need to be provided.One of ordinary skill in the art would readily be capable of determiningthis and providing the necessary signals. It is well known that theinitiation codon must be “in-frame” with the reading frame of thedesired coding sequence to ensure translation of the entire insert. Theexogenous translational control signals and initiation codons can beeither natural or synthetic. The efficiency of expression may beenhanced by the inclusion of appropriate transcription enhancerelements.

In certain embodiments of the invention, the use of internal ribosomeentry sites (IRES) elements are used to create multigene, orpolycistronic, messages. IRES elements are able to bypass the ribosomescanning model of 5′—methylated Cap dependent translation and begintranslation at internal sites (Pelletier and Sonenberg, 1988). IRESelements from two members of the picornavirus family (polio andencephalomyocarditis) have been described (Pelletier and Sonenberg,1988), as well an IRES from a mammalian message (Macejak and Sarnow,1991). IRES elements can be linked to heterologous open reading frames.Multiple open reading frames can be transcribed together, each separatedby an IRES, creating polycistronic messages. By virtue of the IRESelement, each open reading frame is accessible to ribosomes forefficient translation. Multiple genes can be efficiently expressed usinga single promoter/enhancer to transcribe a single message (see U.S. Pat.Nos. 5,925,565 and 5,935,819, each herein incorporated by reference).

c. Multiple Cloning Sites

Vectors can include a multiple cloning site (MCS), which is a nucleicacid region that contains multiple restriction enzyme sites, any ofwhich can be used in conjunction with standard recombinant technology todigest the vector (see, for example, Carbonelli et al., 1999, Levensonet al., 1998, and Cocea, 1997, incorporated herein by reference.)“Restriction enzyme digestion” refers to catalytic cleavage of a nucleicacid molecule with an enzyme that functions only at specific locationsin a nucleic acid molecule. Many of these restriction enzymes arecommercially available. Use of such enzymes is widely understood bythose of skill in the art. Frequently, a vector is linearized orfragmented using a restriction enzyme that cuts within the MCS to enableexogenous sequences to be ligated to the vector. “Ligation” refers tothe process of forming phosphodiester bonds between two nucleic acidfragments, which may or may not be contiguous with each other.Techniques involving restriction enzymes and ligation reactions are wellknown to those of skill in the art of recombinant technology.

d. Splicing Sites

Most transcribed eukaryotic RNA molecules will undergo RNA splicing toremove introns from the primary transcripts. Vectors containing genomiceukaryotic sequences may require donor and/or acceptor splicing sites toensure proper processing of the transcript for protein expression (see,for example, Chandler et al., 1997, herein incorporated by reference).

e. Termination Signals

The vectors or constructs of the present invention will generallycomprise at least one termination signal. A “termination signal” or“terminator” is comprised of the DNA sequences involved in specifictermination of an RNA transcript by an RNA polymerase. Thus, in certainembodiments a termination signal that ends the production of an RNAtranscript is contemplated. A terminator may be necessary in vivo toachieve desirable message levels.

In eukaryotic systems, the terminator region may also comprise specificDNA sequences that permit site-specific cleavage of the new transcriptso as to expose a polyadenylation site. This signals a specializedendogenous polymerase to add a stretch of about 200 A residues (polyA)to the 3′ end of the transcript. RNA molecules modified with this polyAtail appear to more stable and are translated more efficiently. Thus, inother embodiments involving eukaryotes, it is preferred that thatterminator comprises a signal for the cleavage of the RNA, and it ismore preferred that the terminator signal promotes polyadenylation ofthe message. The terminator and/or polyadenylation site elements canserve to enhance message levels and to minimize read through from thecassette into other sequences.

Terminators contemplated for use in the invention include any knownterminator of transcription described herein or known to one of ordinaryskill in the art, including but not limited to, for example, thetermination sequences of genes, such as for example the bovine growthhormone terminator or viral termination sequences, such as for examplethe SV40 terminator. In certain embodiments, the termination signal maybe a lack of transcribable or translatable sequence, such as due to asequence truncation.

f. Polyadenylation Signals

In expression, particularly eukaryotic expression, one will typicallyinclude a polyadenylation signal to effect proper polyadenylation of thetranscript. The nature of the polyadenylation signal is not believed tobe crucial to the successful practice of the invention, and any suchsequence may be employed. Preferred embodiments include the SV40polyadenylation signal or the bovine growth hormone polyadenylationsignal, convenient and known to function well in various target cells.Polyadenylation may increase the stability of the transcript or mayfacilitate cytoplasmic transport.

g. Origins of Replication

In order to propagate a vector in a host cell, it may contain one ormore origins of replication sites (often termed “ori”), which is aspecific nucleic acid sequence at which replication is initiated.Alternatively an autonomously replicating sequence (ARS) can be employedif the host cell is yeast.

h. Selectable and Screenable Markers

In certain embodiments of the invention, cells containing a nucleic acidconstruct of the present invention may be identified in vitro or in vivoby including a marker in the expression vector. Such markers wouldconfer an identifiable change to the cell permitting easy identificationof cells containing the expression vector. Generally, a selectablemarker is one that confers a property that allows for selection. Apositive selectable marker is one in which the presence of the markerallows for its selection, while a negative selectable marker is one inwhich its presence prevents its selection. An example of a positiveselectable marker is a drug resistance marker.

Usually the inclusion of a drug selection marker aids in the cloning andidentification of transformants, for example, genes that conferresistance to neomycin, puromycin, hygromycin, DHFR, GPT, zeocin andhistidinol are useful selectable markers. In addition to markersconferring a phenotype that allows for the discrimination oftransformants based on the implementation of conditions, other types ofmarkers including screenable markers such as GFP, whose basis iscolorimetric analysis, are also contemplated. Alternatively, screenableenzymes such as herpes simplex virus thymidine kinase (tk) orchloramphenicol acetyltransferase (CAT) may be utilized. One of skill inthe art would also know how to employ immunologic markers, possibly inconjunction with FACS analysis. The marker used is not believed to beimportant, so long as it is capable of being expressed simultaneouslywith the nucleic acid encoding a gene product. Further examples ofselectable and screenable markers are well known to one of skill in theart.

i. Plasmid Vectors

In certain embodiments, a plasmid vector is contemplated for use totransform a host cell. In general, plasmid vectors containing repliconand control sequences which are derived from species compatible with thehost cell are used in connection with these hosts. The vector ordinarilycarries a replication site, as well as marking sequences which arecapable of providing phenotypic selection in transformed cells. In anon-limiting example, E. coli is often transformed using derivatives ofpBR322, a plasmid derived from an E. coli species. pBR322 contains genesfor ampicillin and tetracycline resistance and thus provides easy meansfor identifying transformed cells. The pBR plasmid, or other microbialplasmid or phage must also contain, or be modified to contain, forexample, promoters which can be used by the microbial organism forexpression of its own proteins.

In addition, phage vectors containing replicon and control sequencesthat are compatible with the host microorganism can be used astransforming vectors in connection with these hosts. For example, thephage lambda GEM™-11 may be utilized in making a recombinant phagevector which can be used to transform host cells, such as, for example,E. coli LE392.

Further useful plasmid vectors include pIN vectors (Inouye et al.,1985); and pGEX vectors, for use in generating glutathione S-transferase(GST) soluble fusion proteins for later purification and separation orcleavage. Other suitable fusion proteins are those with β-galactosidase,ubiquitin, and the like.

Bacterial host cells, for example, E. coli, comprising the expressionvector, are grown in any of a number of suitable media, for example, LB.The expression of the recombinant protein in certain vectors may beinduced, as would be understood by those of skill in the art, bycontacting a host cell with an agent specific for certain promoters,e.g., by adding IPTG to the media or by switching incubation to a highertemperature. After culturing the bacteria for a further period,generally of between 2 and 24 h, the cells are collected bycentrifugation and washed to remove residual media.

j. Viral Vectors

The ability of certain viruses to infect cells or enter cells viareceptor-mediated endocytosis, and to integrate into host cell genomeand express viral genes stably and efficiently have made them attractivecandidates for the transfer of foreign nucleic acids into cells (e.g.,mammalian cells). Non-limiting examples of virus vectors that may beused to deliver a nucleic acid of the present invention are describedbelow.

1. Adenoviral Vectors

A particular method for delivery of the nucleic acid involves the use ofan adenovirus expression vector. Although adenovirus vectors are knownto have a low capacity for integration into genomic DNA, this feature iscounterbalanced by the high efficiency of gene transfer afforded bythese vectors. “Adenovirus expression vector” is meant to include thoseconstructs containing adenovirus sequences sufficient to (a) supportpackaging of the construct and (b) to ultimately express a tissue orcell-specific construct that has been cloned therein. Knowledge of thegenetic organization or adenovirus, a 36 kb, linear, double-stranded DNAvirus, allows substitution of large pieces of adenoviral DNA withforeign sequences up to 7 kb (Grunhaus and Horwitz, 1992).

2. AAV Vectors

The nucleic acid may be introduced into the cell using adenovirusassisted transfection. Increased transfection efficiencies have beenreported in cell systems using adenovirus coupled systems (Kelleher andVos, 1994; Cotten et al., 1992; Curiel, 1994). Adeno-associated virus(AAV) is an attractive vector system as it has a high frequency ofintegration and it can infect non-dividing cells, thus making it usefulfor delivery of genes into mammalian cells, for example, in tissueculture (Muzyczka, 1992) or in vivo. AAV has a broad host range forinfectivity (Tratschin et al., 1984; Laughlin et al., 1986; Lebkowski etal., 1988; McLaughlin et al., 1988). Details concerning the generationand use of rAAV vectors are described in U.S. Pat. Nos. 5,139,941 and4,797,368, each incorporated herein by reference.

3. Retroviral Vectors

Retroviruses have promise as gene delivery vectors due to their abilityto integrate their genes into the host genome, transferring a largeamount of foreign genetic material, infecting a broad spectrum ofspecies and cell types and of being packaged in special cell-lines(Miller, 1992).

In order to construct a retroviral vector, a nucleic acid (e.g., oneencoding gene of interest) is inserted into the viral genome in theplace of certain viral sequences to produce a virus that isreplication-defective. In order to produce virions, a packaging cellline containing the gag, pol, and env genes but without the LTR andpackaging components is constructed (Mann et al., 1983). When arecombinant plasmid containing a cDNA, together with the retroviral LTRand packaging sequences is introduced into a special cell line (e.g., bycalcium phosphate precipitation for example), the packaging sequenceallows the RNA transcript of the recombinant plasmid to be packaged intoviral particles, which are then secreted into the culture media (Nicolasand Rubenstein, 1988; Temin, 1986; Mann et al., 1983). The mediacontaining the recombinant retroviruses is then collected, optionallyconcentrated, and used for gene transfer. Retroviral vectors are able toinfect a broad variety of cell types. However, integration and stableexpression require the division of host cells (Paskind et al., 1975).

Lentiviruses are complex retroviruses, which, in addition to the commonretroviral genes gag, pol, and env, contain other genes with regulatoryor structural function. Lentiviral vectors are well known in the art(see, for example, Naldini et al., 1996; Zufferey et al., 1997; Blomeret al., 1997; U.S. Pat. Nos. 6,013,516 and 5,994,136). Some examples oflentivirus include the Human Immunodeficiency Viruses: HIV-1, HIV-2 andthe Simian Immunodeficiency Virus: SIV. Lentiviral vectors have beengenerated by multiply attenuating the HIV virulence genes, for example,the genes env, vif, vpr, vpu and nef are deleted making the vectorbiologically safe.

Recombinant lentiviral vectors are capable of infecting non-dividingcells and can be used for both in vivo and ex vivo gene transfer andexpression of nucleic acid sequences. For example, recombinantlentivirus capable of infecting a non-dividing cell wherein a suitablehost cell is transfected with two or more vectors carrying the packagingfunctions, namely gag, poi and env, as well as rev and tat is describedin U.S. Pat. No. 5,994,136, incorporated herein by reference. One maytarget the recombinant virus by linkage of the envelope protein with anantibody or a particular ligand for targeting to a receptor of aparticular cell-type. By inserting a sequence (including a regulatoryregion) of interest into the viral vector, along with another gene whichencodes the ligand for a receptor on a specific target cell, forexample, the vector is now target-specific.

4. Other Viral Vectors

Other viral vectors may be employed as vaccine constructs in the presentinvention. Vectors derived from viruses such as vaccinia virus(Ridgeway, 1988; Baichwal and Sugden, 1986; Coupar et al., 1988),sindbis virus, cytomegalovirus and herpes simplex virus may be employed.They offer several attractive features for various mammalian cells(Friedmann, 1989; Ridgeway, 1988; Baichwal and Sugden, 1986; Coupar etal., 1988; Horwich et al., 1990).

5. Delivery Using Modified Viruses

A nucleic acid to be delivered may be housed within an infective virusthat has been engineered to express a specific binding ligand. The virusparticle will thus bind specifically to the cognate receptors of thetarget cell and deliver the contents to the cell. A novel approachdesigned to allow specific targeting of retrovirus vectors was developedbased on the chemical modification of a retrovirus by the chemicaladdition of lactose residues to the viral envelope. This modificationcan permit the specific infection of hepatocytes via sialoglycoproteinreceptors.

Another approach to targeting of recombinant retroviruses was designedin which biotinylated antibodies against a retroviral envelope proteinand against a specific cell receptor were used. The antibodies werecoupled via the biotin components by using streptavidin (Roux et al.,1989). Using antibodies against major histocompatibility complex class Iand class II antigens, they demonstrated the infection of a variety ofhuman cells that bore those surface antigens with an ecotropic virus invitro (Roux et al., 1989).

7. Vector Delivery and Cell Transformation

Suitable methods for nucleic acid delivery for transformation of anorganelle, a cell, a tissue or an organism for use with the currentinvention are believed to include virtually any method by which anucleic acid (e.g., DNA) can be introduced into an organelle, a cell, atissue or an organism, as described herein or as would be known to oneof ordinary skill in the art. Such methods include, but are not limitedto, direct delivery of DNA such as by ex vivo transfection (Wilson etal., 1989; Nabel and Baltimore, 1987), by injection (U.S. Pat. Nos.5,994,624, 5,981,274, 5,945,100, 5,780,448, 5,736,524, 5,702,932,5,656,610, 5,589,466 and 5,580,859, each incorporated herein byreference), including microinjection (Harland and Weintraub, 1985; U.S.Pat. No. 5,789,215, incorporated herein by reference); byelectroporation (U.S. Pat. No. 5,384,253, incorporated herein byreference; Tur-Kaspa et al., 1986; Potter et al., 1984); by calciumphosphate precipitation (Graham and Van Der Eb, 1973; Chen and Okayama,1987; Rippe et al., 1990); by using DEAE-dextran followed bypolyethylene glycol (Gopal, 1985); by direct sonic loading (Fechheimeret al., 1987); by liposome mediated transfection (Nicolau and Sene,1982; Fraley et al., 1979; Nicolau et al., 1987; Wong et al., 1980;Kaneda et al., 1989; Kato et al., 1991) and receptor-mediatedtransfection (Wu and Wu, 1987; Wu and Wu, 1988); by microprojectilebombardment (PCT Application Nos. WO 94/09699 and 95/06128; U.S. Pat.Nos. 5,610,042; 5,322,783 5,563,055, 5,550,318, 5,538,877 and 5,538,880,and each incorporated herein by reference); by agitation with siliconcarbide fibers (Kaeppler et al., 1990; U.S. Pat. Nos. 5,302,523 and5,464,765, each incorporated herein by reference); byAgrobacterium-mediated transformation (U.S. Pat. Nos. 5,591,616 and5,563,055, each incorporated herein by reference); by PEG-mediatedtransformation of protoplasts (Omirulleh et al., 1993; U.S. Pat. Nos.4,684,611 and 4,952,500, each incorporated herein by reference); bydesiccation/inhibition-mediated DNA uptake (Potrykus et al., 1985), andany combination of such methods. Through the application of techniquessuch as these, organelle(s), cell(s), tissue(s) or organism(s) may bestably or transiently transformed.

a. Injection

In certain embodiments, a nucleic acid may be delivered to an organelle,a cell, a tissue or an organism via one or more injections (i.e., aneedle injection), such as, for example, subcutaneously, intradermally,intramuscularly, intervenously, intraperitoneally, etc. Methods ofinjection of vaccines are well known to those of ordinary skill in theart (e.g., injection of a composition comprising a saline solution).Further embodiments of the present invention include the introduction ofa nucleic acid by direct microinjection. Direct microinjection has beenused to introduce nucleic acid constructs into Xenopus oocytes (Harlandand Weintraub, 1985).

b. Electroporation

In certain embodiments of the present invention, a nucleic acid isintroduced into an organelle, a cell, a tissue or an organism viaelectroporation. Electroporation involves the exposure of a suspensionof cells and DNA to a high-voltage electric discharge. In some variantsof this method, certain cell wall-degrading enzymes, such aspectin-degrading enzymes, are employed to render the target recipientcells more susceptible to transformation by electroporation thanuntreated cells (U.S. Pat. No. 5,384,253, incorporated herein byreference). Alternatively, recipient cells can be made more susceptibleto transformation by mechanical wounding.

Transfection of eukaryotic cells using electroporation has been quitesuccessful. Mouse pre-B lymphocytes have been transfected with humankappa-immunoglobulin genes (Potter et al., 1984), and rat hepatocyteshave been transfected with the chloramphenicol acetyltransferase gene(Tur-Kaspa et al., 1986) in this manner.

c. Calcium Phosphate

In other embodiments of the present invention, a nucleic acid isintroduced to the cells using calcium phosphate precipitation. Human KBcells have been transfected with adenovirus 5 DNA (Graham and Van DerEb, 1973) using this technique. Also in this manner, mouse L(A9), mouseC127, CHO, CV-1, BHK, NIH3T3 and HeLa cells were transfected with aneomycin marker gene (Chen and Okayama, 1987), and rat hepatocytes weretransfected with a variety of marker genes (Rippe et al., 1990).

d. DEAE-Dextran

In another embodiment, a nucleic acid is delivered into a cell usingDEAE-dextran followed by polyethylene glycol. In this manner, reporterplasmids were introduced into mouse myeloma and erythroleukemia cells(Gopal, 1985).

e. Sonication Loading

Additional embodiments of the present invention include the introductionof a nucleic acid by direct sonic loading. LTK⁻ fibroblasts have beentransfected with the thymidine kinase gene by sonication loading(Fechheimer et al., 1987).

f. Liposome-Mediated Transfection

In a further embodiment of the invention, a nucleic acid may beentrapped in a lipid complex such as, for example, a liposome. Liposomesare vesicular structures characterized by a phospholipid bilayermembrane and an inner aqueous medium. Multilamellar liposomes havemultiple lipid layers separated by aqueous medium. They formspontaneously when phospholipids are suspended in an excess of aqueoussolution. The lipid components undergo self-rearrangement before theformation of closed structures and entrap water and dissolved solutesbetween the lipid bilayers (Ghosh and Bachhawat, 1991). Alsocontemplated is an nucleic acid complexed with Lipofectamine (Gibco BRL)or Superfect (Qiagen).

Liposome-mediated nucleic acid delivery and expression of foreign DNA invitro has been very successful (Nicolau and Sene, 1982; Fraley et al.,1979; Nicolau et al., 1987). The feasibility of liposome-mediateddelivery and expression of foreign DNA in cultured chick embryo, HeLaand hepatoma cells has also been demonstrated (Wong et al., 1980).

In certain embodiments of the invention, a liposome may be complexedwith a hemagglutinating virus (HVJ). This has been shown to facilitatefusion with the cell membrane and promote cell entry ofliposome-encapsulated DNA (Kaneda et al., 1989). In other embodiments, aliposome may be complexed or employed in conjunction with nuclearnon-histone chromosomal proteins (HMG-1) (Kato et al., 1991). In yetfurther embodiments, a liposome may be complexed or employed inconjunction with both HVJ and HMG-1. In other embodiments, a deliveryvehicle may comprise a ligand and a liposome.

g. Receptor Mediated Transfection

Still further, a nucleic acid may be delivered to a target cell viareceptor-mediated delivery vehicles. These take advantage of theselective uptake of macromolecules by receptor-mediated endocytosis thatwill be occurring in a target cell. In view of the cell type-specificdistribution of various receptors, this delivery method adds anotherdegree of specificity to the present invention.

Certain receptor-mediated gene targeting vehicles comprise a cellreceptor-specific ligand and a nucleic acid-binding agent. Otherscomprise a cell receptor-specific ligand to which the nucleic acid to bedelivered has been operatively attached. Several ligands have been usedfor receptor-mediated gene transfer (Wu and Wu, 1987; Wagner et al.,1990; Perales et al., 1994; Myers, EPO 0273085), which establishes theoperability of the technique. Specific delivery in the context ofanother mammalian cell type has been described (Wu and Wu, 1993;incorporated herein by reference). In certain aspects of the presentinvention, a ligand will be chosen to correspond to a receptorspecifically expressed on the target cell population.

In other embodiments, a nucleic acid delivery vehicle component of acell-specific nucleic acid targeting vehicle may comprise a specificbinding ligand in combination with a liposome. The nucleic acid(s) to bedelivered are housed within the liposome and the specific binding ligandis functionally incorporated into the liposome membrane. The liposomewill thus specifically bind to the receptor(s) of a target cell anddeliver the contents to a cell. Such systems have been shown to befunctional using systems in which, for example, epidermal growth factor(EGF) is used in the receptor-mediated delivery of a nucleic acid tocells that exhibit upregulation of the EGF receptor.

In still further embodiments, the nucleic acid delivery vehiclecomponent of a targeted delivery vehicle may be a liposome itself, whichwill preferably comprise one or more lipids or glycoproteins that directcell-specific binding. For example, lactosyl-ceramide, agalactose-terminal asialganglioside, have been incorporated intoliposomes and observed an increase in the uptake of the insulin gene byhepatocytes (Nicolau et al., 1987). It is contemplated that thetissue-specific transforming constructs of the present invention can bespecifically delivered into a target cell in a similar manner.

h. Microprojectile Bombardment

Microprojectile bombardment techniques can be used to introduce anucleic acid into at least one, organelle, cell, tissue or organism(U.S. Pat. Nos. 5,550,318, 5,538,880, 5,610,042, and PCT Application WO94/09699; each of which is incorporated herein by reference). Thismethod depends on the ability to accelerate DNA-coated microprojectilesto a high velocity allowing them to pierce cell membranes and entercells without killing them (Klein et al., 1987). There are a widevariety of microprojectile bombardment techniques known in the art, manyof which are applicable to the invention.

In this microprojectile bombardment, one or more particles may be coatedwith at least one nucleic acid and delivered into cells by a propellingforce. Several devices for accelerating small particles have beendeveloped. One such device relies on a high voltage discharge togenerate an electrical current, which in turn provides the motive force(Yang et al., 1990). The microprojectiles used have consisted ofbiologically inert substances such as tungsten or gold particles orbeads. Exemplary particles include those comprised of tungsten,platinum, and preferably, gold. It is contemplated that in someinstances DNA precipitation onto metal particles would not be necessaryfor DNA delivery to a recipient cell using microprojectile bombardment.However, it is contemplated that particles may contain DNA rather thanbe coated with DNA. DNA-coated particles may increase the level of DNAdelivery via particle bombardment but are not, in and of themselves,necessary.

For the bombardment, cells in suspension are concentrated on filters orsolid culture medium. Alternatively, immature embryos or other targetcells may be arranged on solid culture medium. The cells to be bombardedare positioned at an appropriate distance below the macroprojectilestopping plate.

An illustrative embodiment of a method for delivering DNA into a cell(e.g., a plant cell) by acceleration is the Biolistics Particle DeliverySystem, which can be used to propel particles coated with DNA or cellsthrough a screen, such as a stainless steel or Nytex screen, onto afilter surface covered with cells, such as for example, a monocot plantcells cultured in suspension. The screen disperses the particles so thatthey are not delivered to the recipient cells in large aggregates. It isbelieved that a screen intervening between the projectile apparatus andthe cells to be bombarded reduces the size of projectiles aggregate andmay contribute to a higher frequency of transformation by reducing thedamage inflicted on the recipient cells by projectiles that are toolarge.

VII. Pharmaceutical Formulations and Routes of Administration

Where clinical applications are contemplated, it will be necessary toprepare pharmaceutical compositions in a form appropriate for theintended application. Generally, this will entail preparing compositionsthat are essentially free of pyrogens, as well as other impurities thatcould be harmful to humans or animals.

The phrase “pharmaceutically or pharmacologically acceptable” refer tomolecular entities and compositions that do not produce adverse,allergic, or other untoward reactions when administered to an animal ora human. As used herein, “pharmaceutically acceptable carrier” includesany and all solvents, dispersion media, coatings, antibacterial andantifungal agents, isotonic and absorption delaying agents and the like.The use of such media and agents for pharmaceutically active substancesis well known in the art. Supplementary active ingredients also can beincorporated into the compositions.

Administration of these compositions according to the present inventionwill be via any common route so long as the target tissue is availablevia that route. This includes intradermal, subcutaneous, intramuscular,intraperitoneal or intravenous injection. In particular, intratumoralroutes and sites local and regional to tumors are contemplated. Suchcompositions would normally be administered as pharmaceuticallyacceptable compositions, described supra.

The active compounds also may be administered parenterally orintraperitoneally. Solutions of the active compounds as free base orpharmacologically acceptable salts can be prepared in water suitablymixed with a surfactant, such as hydroxypropylcellulose. Dispersions canalso be prepared in glycerol, liquid polyethylene glycols, and mixturesthereof and in oils. Under ordinary conditions of storage and use, thesepreparations contain a preservative to prevent the growth ofmicroorganisms.

The pharmaceutical forms suitable for injectable use include sterileaqueous solutions or dispersions and sterile powders for theextemporaneous preparation of sterile injectable solutions ordispersions. In all cases the form must be sterile and must be fluid tothe extent that easy administration by a syringe is possible. It must bestable under the conditions of manufacture and storage and must bepreserved against the contaminating action of microorganisms, such asbacteria and fungi. The carrier can be a solvent or dispersion mediumcontaining, for example, water, ethanol, polyol (for example, glycerol,propylene glycol, and liquid polyethylene glycol, and the like),suitable mixtures thereof, and vegetable oils. The proper fluidity canbe maintained, for example, by the use of a coating, such as lecithin,by the maintenance of the required particle size in the case ofdispersion and by the use of surfactants. The prevention of the actionof microorganisms can be brought about by various antibacterial anantifungal agents, for example, parabens, chlorobutanol, phenol, sorbicacid, thimerosal, and the like. In many cases, it will be preferable toinclude isotonic agents, for example, sugars or sodium chloride.Prolonged absorption of the injectable compositions can be brought aboutby the use in the compositions of agents delaying absorption, forexample, aluminum monostearate and gelatin.

Sterile injectable solutions are prepared by incorporating the activecompounds in the required amount in the appropriate solvent with variousof the other ingredients enumerated above, as required, followed byfiltered sterilization. Generally, dispersions are prepared byincorporating the various sterilized active ingredients into a sterilevehicle which contains the basic dispersion medium and the requiredother ingredients from those enumerated above. In the case of sterilepowders for the preparation of sterile injectable solutions, thepreferred methods of preparation are vacuum-drying and freeze-dryingtechniques which yield a powder of the active ingredient plus anyadditional desired ingredient from a previously sterile-filteredsolution thereof.

For oral administration the polypeptides of the present invention may beincorporated with excipients that may include water, binders, abrasives,flavoring agents, foaming agents, and humectants.

As used herein, “pharmaceutically acceptable carrier” includes any andall solvents, dispersion media, coatings, antibacterial and antifungalagents, isotonic and absorption delaying agents and the like. The use ofsuch media and agents for pharmaceutical active substances is well knownin the art. Except insofar as any conventional media or agent isincompatible with the active ingredient, its use in the therapeuticcompositions is contemplated. Supplementary active ingredients can alsobe incorporated into the compositions.

The compositions of the present invention may be formulated in a neutralor salt form. Pharmaceutically-acceptable salts include the acidaddition salts (formed with the free amino groups of the protein) andwhich are formed with inorganic acids such as, for example, hydrochloricor phosphoric acids, or such organic acids as acetic, oxalic, tartaric,mandelic, and the like. Salts formed with the free carboxyl groups canalso be derived from inorganic bases such as, for example, sodium,potassium, ammonium, calcium, or ferric hydroxides, and such organicbases as isopropylamine, trimethylamine, histidine, procaine and thelike.

VIII. Examples

The following examples are included to demonstrate preferred embodimentsof the invention. It should be appreciated by those of skill in the artthat the techniques disclosed in the examples which follow representtechniques discovered by the inventor to function well in the practiceof the invention, and thus can be considered to constitute preferredmodes for its practice. However, those of skill in the art should, inlight of the present disclosure, appreciate that many changes can bemade in the specific embodiments which are disclosed and still obtain alike or similar result without departing from the spirit and scope ofthe invention.

Example 1 Materials and Methods

Materials. The MALDI matrix compound 3,5-dimethoxy-4-hydroxycinnamicacid (sinapinic acid, SA), hematoxylin, eosin, phenylmethylsulfonylfluoride (PMSF), sodium chloride and ammonium bicarbonate were purchasedfrom Sigma Chemical Co. (St. Louis, Mo.). Dulbecco's Modified Eagle'sMedium (DMEM) was from Life Technologies, Inc. (Rockville, Md.) andfetal bovine serum (FBS) was from Gemini Bio-Products (Woodland,Calif.). T-PER extraction buffer was purchased from PierceBiotechnology, Inc. (Rockford, Ill.). Sucrose, ammonium acetate andultrapure Tris were obtained from J. T. Baker (Phillipsburg, N.J.).Sequencing grade trifluoroacetic acid (TFA) was from Burdick and Jackson(Muskegon, Mich.). HPLC grade acetonitrile was purchased from EM Science(Merck, Darmstadt, Germany). Sequencing grade trypsin was from Promega(Madison, Wis.) and Anti-PEA-15 from Santa Cruz Biotechnology, Inc.(Santa Cruz, Calif.).

Collecting and Processing Clinical Material and Patient Information.Tissues were obtained, with informed consent and IRB approval, frompatients undergoing tumor resection or other surgical procedures atVanderbilt University Medical Center, Cleveland Clinical Foundation andthe National Institutes of Health. A total of 162 tissue samples from127 patients including 19 patients undergoing respective surgery fornon-neoplastic disease, 29 grade II, 22 grade III, and 57 grade IVglioma patients were analyzed. Patient information was collectedincluding gender, age, treatment received before and after surgery,extent of surgery, current status (alive, alive with progressivedisease, deceased and cause of death), and survival from the time oforiginal pathological diagnosis. Samples were collected at the time ofsurgery, immediately snap-frozen in liquid nitrogen, and stored at −80°C. until analysis. Histopathological diagnoses were made by aneuropathologist, blinded to the original clinical diagnosis, fromsubsequent H & E stained sections according to the 2000 WHOclassification (Klieihues and Cavenee, 2000) as previously described(Schwatrtz et al., 2004).

Samples were prepared for MALDI analysis as described previously(Schwatrtz et al., 2004; Schwartz et al., 2003). Briefly, frozen tissueswere sectioned and transferred to MALDI target plates. Matrix droplets(0.1 μl saturated SA in 50:50 acetonitrile:0.1% TFA in water, v/v) wereblindly deposited on the surface of the sample, and the sections weredried. Optical section images were taken to align MS analysis regionswith cellular morphology determined by histology. Samples were analyzedin a blinded fashion without knowledge of histological diagnosis orclinical data.

Mass Spectrometry Analysis and Data Processing. Each matrix droplet wasanalyzed on a MALDI TOF (time-of-flight) Voyager DE-STR massspectrometer (Applied Biosystems, Foster City, Calif.) as describedpreviously (Schwatrtz et al., 2004). Spectra were internally masscalibrated using the singly- and doubly-charged ions for α-hemoglobin(m/z 7564.2 and 15127.4 respectively), ubiquitin (m/z 8565.8), andthymosin β4 (m/z 4964.5, previously identified in human glioblastomaxenographs (Stoeckli et al., 2001). Mass spectra were baselinecorrected, smoothed, and normalized. The peak lists from each individualbiopsy or patient, depending on the analysis approach, were averaged togenerate one general protein profile.

Statistical Data Analysis. Two independent supervised methods, symbolicdiscriminant analysis (SDA) (Moore et al., 2002) and the weightedflexible compound covariate method (WFCCM) (Shyr and KyungMann, 2003),were used to analyze the protein profiles. SDA applies geneticprogramming to determine discriminatory signals and builds functionsusing these signals that distinguish sample populations based on theirclassification. WFCCM applies multiple statistical tests to determinediscriminatory markers. A linear combination of these markers is thengenerated that differentiates the sample groups. Further information isincluded in the supplementary data.

Protein Marker Identification. Two samples were used for proteinidentification, a glioma cell line and a human glioma sample. Theglioblastoma cell line, U118 MG, (American Type Culture Collection,Manassas, Va.) was cultured in DMEM supplemented with 10% FBS andharvested using an extraction buffer (0.25 M sucrose, 0.01 M Tris-HCLand 0.1 mM PMSF, pH 7.6 at 4° C.). A cell aliquot was mixed 1:1 (v/v)with the extraction buffer, homogenized in an ice-chilled Duallhomogenizer and centrifuged at 10,000 g for 10 min at 4° C. Thesupernatant was collected for protein identification. A glioblastoma(grade IV glioma) tissue was collected at the time of surgery, frozenand stored at −80° C. The tissue was homogenized in T-PER extractionbuffer (50 mg of tissue per 1 mL of T-PER) in an ice-chilled Duallhomogenizer and centrifuged at 16,000 g for 30 min at 4° C. Thesupernatant was collected for protein identification.

Both samples were separated in two-dimensions, first by ion exchangechromatography followed by reverse-phase high-performance liquidchromatography (HPLC). The cell line supernatant was separated by anionexchange chromatography using a HiTrap Q HP anion exchange column(Amersham Biosciences, Uppsala, Sweden) and a NaCl gradient (0.05 M, 0.1M, 0.15 M, 0.2 M, 0.25 M, 0.3 M, 0.35 M, 0.45 M, 0.55 M, and 1 M NaCl)based on the extraction solution. HPLC separation for selected fractionswas achieved over a Vydac (Hesperia, Calif.) 214MS52 reverse phase C4column (5 μm particles, 2.1 mm×25 cm) at 40° C. using a linear gradientof 5% B to 20% B over 11 min, 20% B to 30% B over 15 min, 30% B to 55% Bover 90 min, and 55% B to 95% B over 10 min. For fraction separation,solvent A was 0.1% TFA and solvent B was 0.1% TFA in acetonitrile. Thetissue sample supernatant was separated by cation exchangechromatography using a HiTrap SP HP cation exchange column (AmershamBiosciences, Uppsala, Sweden) with a linear gradient of 0% B to 100% Bover 15 min, where A was 10 mM ammonium acetate and B was 1 M NaCl in 10mM ammonium acetate, pH 3.8 at room temperature. Selected fractions wereseparated over a Vydac (Hesperia, Calif.) 214MS5115 reverse phase C4column (5 μm particles, 1 mm×15 cm) at 40° C. using a linear gradient of5% B to 25% B over 5 min, 25% B to 60% B over 50 min, and 60% B to 95% Bover 20 min. Fractions were analyzed by MALDI MS for the markers ofinterest after each separation. HPLC fractions of interest werereconstituted in 0.1 M ammonium bicarbonate and digested with trypsin(1:50, trypsin:protein, w/w; 37° C.; 16-20 hrs). Digested fragments wereanalyzed using either an Applied Biosystems 4700 MALDI TOF/TOF massspectrometer (Foster City, Calif.) or a ThermoLTQ ion trap massspectrometer equipped with a Thermo Surveyor LC pump and amicroelectrospray source (Thermo Electron, San Jose, Calif.).

MS and MS-MS spectra from MALDI TOF/TOF analysis were collected and theproteins were identified as previously described (Friedman et al.,2004). The data were searched against the human NCBI database using theMascot (www.matrixscience.com) database search algorithm. A significancecut-off score of 65 was used. Analysis on the ThermoLTQ massspectrometer was performed using one full MS scan followed by threeMS-MS scans of the three most intense ions. MS-MS spectra were searchedagainst the human database using SEQUEST (Thermo Electron, San Jose,Calif.) and the Sequest search outputs were filtered using acustom-designed software tool called CHIPS (Complete HeirarchicalIntegration of Protein Searches) using the following filtering criteria:cross correlation (X_(corr)) value of >1.0 for singly charged ions, >1.8for doubly charged ions, and >2.5 for triply charged ion. In addition, aRSp (ranking of preliminary score) value of <5 and a Sp value(preliminary score)>350 were required for positive peptideidentifications. A minimum of two peptide matches and a positivecorrelation between the m/z ratio detected and the MW of the intactprotein (including post-translational modifications) were also requiredfor protein identification.

Immunohistochemistry. For immunofluorescence histochemistry, 18 μm thicksections were cut on a cryostat and incubated for 24 hours with PEA-15antibodies (1:1000). The sections were washed and incubated withCy3-conjugated anti-mouse secondary antibodies (1:1600; JacksonImmunoResearch), washed, mounted, and coverslipped.

Example 2 Results

Mass Spectrometric Profiling of Human Brain Tissues. A total of 162tissue samples from 127 patients (108 glioma and 19 non-tumor patients)were collected and analyzed by mass spectrometry. The general protocolis presented (FIG. 1). Tissue sections were coated with matrix droplets(typically 5-10 droplets were deposited on each section) and eachdroplet was directly analyzed by MALDI MS; serial sections werecollected and stained with hematoxylin and eosin for histopathology.Over 1000 individual mass spectra, representing non-tumor cellpopulations from non-tumor patients or tumor cell populations fromglioma patients, were used for comparative analysis. Between 300 and 500individual protein signals in the mass/charge (m/z) range of 2,000 to70,000 were detected; an example of the protein profile complexity,generated by MS analysis of a 12 μm human glioma section, is presented(FIG. 2). The intensity scale was expanded to display low intensity ionsignals. The inset, displaying the m/z range 6000 to 8000, furtherdemonstrates the complexity of the data collected. The spectra wereprocessed and multiple spectra were averaged to generate one peak listper patient or tissue sample, depending on the statistical analysisperformed. To determine the variability of our tissue profilingapproach, the average intra-class agreement rate (protein patternvariations within a patient sample) was measured to be 91.3%+/−2.6% (95%CI: 87.2%, 95.4%). This measurement suggests a relative consistency,spectrum-to-spectrum, within a given tissue sample.

Correlating Protein Pattern Changes to Glioma Classifications. Initialdata analysis focused on verifying that direct-tissue MALDI massspectrometric analysis could be used for tissue classification.Supervised classification analysis was performed to identify tumorclassification-distinctive biomarker patterns, verified by histology.Data was processed, averaged by biopsy, and grouped into one of fourcategories: non-tumor tissue (26 samples), grade II tumor (35 samples),grade III tumor (28 samples) and grade IV tumor (73 samples). Non-tumortissue refers to samples collected from patients undergoing surgicalresection for non-neoplastic processes. For statistical analysis,biopsies were separated into training and testing data sets, consistingof ⅔ and ⅓ of the samples per classification, respectively.

Pairwise comparisons were performed on the training set to identify asubset of differentially expressed protein signals that best separatedeach classification: non-tumor vs. grades II, III and IV biopsies;non-tumor vs. each individual tumor grade; grade II vs. grade III; gradeII vs. grade IV; grade III vs. grade IV; and grade II, III vs. grade IV.Two independent methods were utilized for data analysis: symbolicdiscriminant analysis (SDA) (Moore et al., 2002) and the weightedflexible compound covariate method (WFCCM) (Shyr and KyungMann, 2003).SDA utilizes genetic programming to build functions, based on determineddiscriminatory signals, which distinguish sample classifications. WFCCMgenerates a model, based on a linear combination ofstatistically-determined discriminatory markers, which distinguishessample groups.

For each analysis approach, a model was defined that best classifiedsamples in the training data set. Based on the model, each patient wasassigned a score using the expression, or signal intensity, of thedetermined biomarker signals; the accuracy of this classification schemewas verified on a blind data set (testing data set). The results fromthese analyses are summarized (Table 2). Classification and predictionaccuracies are defined as the number of samples in the training andtesting data sets, respectively, correctly classified. Biopsy proteinpatterns reflect a strong separation between tumor and non-tumor tissuesthat extends to individual tumor grades. In all cases, non-tumor tissuescould be distinguished from gliomas with >92% classification accuracy.When comparing gliomas of different grades, the best separation was seenwhen comparing grade II and grade IV tumors (>93% classificationaccuracy), with slightly lower values for the grade III vs. grade IV andgrade II, III vs. grade IV. The most difficult comparison was betweengrade II and grade III, which recapitulates the clinical situation.Accuracy limitations in protein profiling are due, in part, to theinfiltrative nature of these tumors, the heterogeneous nature of thecells that comprise gliomas, and some methodological limitations.Nonetheless, the results compare favorably to studies of inter-classobserver variability in pathology and neuropathology (Aldape et al.,2000; Castillo et al., 2004).

TABLE 2 SDA WFCCM Data Set No. Classification Prediction No.Classification Prediction (# Biopsies Training; Biomarkers AccuracyAccuracy Biomarkers Accuracy Accuracy Analysis Testing Set) Determined(%) (%) Determined (%) (%) NT/T 18/91; 8/45 2 92 89 28 96 92 NT/TII18/24; 8/11 2 92 84 26 100 84 NT/TIII 18/17; 8/11 4 94 95 38 97 89NT/TIV 18/50; 8/23 2 96 84 42 99 87 TII/TIII 24/17; 11/11 2 76 77 61 8850 TII/TIV 24/50; 11/23 3 93 82 17 97 82 TIII/TIV 17/50; 11/23 4 85 8032 96 76 TII, III/TIV 41/50; 22/73 1 79 80 62 93 78

Interestingly, both analyses exhibited similar abilities in segregatingthe individual classifications. Models from SDA and WFCCM performed wellin distinguishing non-tumor from tumor and generally separatingindividual tumor grades, but performed poorly in segregating grade IIfrom grade III. While the marker patterns determined by SDA and WFCCMwere distinct, 35% of the classification-specific markers determinedusing SDA were also selected by WFCCM. These results suggest thatclassification based on protein profiling may be independent of thestatistical analysis technique used.

An independent agglomerative hierarchical clustering algorithm verifiedthe statistically significant discriminator protein patterns, determinedby WFCCM, in the training cohort for each of the classificationsperformed. The results of three of these, NT vs. T, NT vs. T_(IV) andT_(II) vs. T_(IV) are shown (FIGS. 3A, 3B and 3C, respectively).Clustering patterns reflect the strong correlation between the MSprotein profile and the tissue classifications.

Correlating Protein Pattern Changes to Glioma Patient Survival.Statistical analysis was then applied to the entire tumor data set of108 glioma patients, with the spectra averaged by patient, to identifybiomarker patterns that correlate to patient survival trends. UsingWFCCM, a summary survival score was determined for each patient based onthe statistically-determined significant protein signals. Patients werethen separated into short-term and long-term prognostic groups using asensitivity analysis according to their correlated protein and survivalpatterns (FIGS. 4A-B). A proteomic pattern of 24 distinct MS signalsdistinguished patients based on survival trends from the time ofpathological diagnosis into two groups, a short-term (STS, meansurvival<15 months) and a long-term (LTS, mean survival>90 months)survival group. Seventeen of these markers were not determined as tumoror tumor-grade specific discriminatory markers in the previous analysis.Survival signal differences include an overexpression of m/z 9747 and10092 in the STS group and an overexpression of m/z 10262 in the LTSgroup. Within the total tumor patient population, analysis identified 52patients in the STS prognostic group and 56 patients in the LTSprognostic group, with P<0.0001. Univariate analysis demonstrated apositive correlation (P<0.01) between advanced patient age, increasingtumor grade, tumors with an astrocytic lineage and shorter survivaltrends. Taking these factors in account, a multivariate Cox proportionalhazards model showed a strong correlation between the MS protein patternand patient survival after adjustment for patient age, gender, tumorsubtype, tumor grade, extent of tumor resection and the use of radiationand chemotherapy treatments pre- and post-surgery. Therefore, theprotein pattern served as an independent indicator of patient survival.The key patient survival variables are shown in a modified model (Table3). Survival analysis of the glioma population from the time of surgery,in which the analyzed sample was resected, was also performed withsimilar results (data not shown).

TABLE 3 Variable H.R. P-value 95% CI Grade II, III and IV Gliomas MSProtein Pattern 1.002 <0.0001 (1.001, 1.003) Age 1.034 0.0177 (1.006,1.062) Gender 0.926 0.8366 (0.445, 1.928) Chemotherapy 0.296 0.0184(0.107, 0.814) Radiation 1.402 0.4697 (0.561, 3.500) Tumor Grade 4.5810.0100 (1.440, 14.575) Grade IV Gliomas MS Protein Pattern 1.014 0.0001(1.007, 1.021) Age 1.063 0.0006 (1.026, 1.021) Gender 1.551 0.3485(0.620, 3.879) Chemotherapy 0.898 0.8349 (0.327, 2.467) Radiation 0.7990.6728 (0.281, 2.268)

Glioblastoma multiforme (GBM), the most common and malignant form ofglioma, is also one of the most rapidly fatal of all human malignancies;median survival after diagnosis for these tumors is measured in months.For patients with a GBM, age, clinical performance status and extent ofsurgical resection are the principal, well-validated prognosticvariables. WFCCM analysis was used to determine whether protein patternscould further differentiate patients based on survival from the time ofGBM presentation. A proteomic pattern of 2 distinct MS signals wasidentified that segregated the patients into a STS (average survival,10.9 months) and LTS group (average survival, 16.8 months). Neither ofthese signals was identified as a significant discriminatory marker inthe previous analyses. A total of 28 of the 57 patients were classifiedinto the STS group and 29 patients in the LTS group (P<0.0001). While anindependent correlation existed between increasing patient age andshorter survival trends, the protein pattern performed as a powerful,independent predictor of patient survival. A multivariate Coxproportional hazards model demonstrated a strong correlation between theMS protein pattern and patient survival after adjustment for patientage, gender, extent of tumor resection, histological subtype, and theuse of radiation and chemotherapy treatments. A modified form of thismodel is presented (Table 3).

Identifying Glioma Biomarkers. Discriminatory protein identification wasconfirmed using two protein sources, the malignant human glioma cellline, U118 MG, and a primary human grade IV glioblastoma sample. Boththe cells and the tissue sample were homogenized and proteins separatedusing a two-dimensional LC approach, consisting of an ion exchangeseparation followed by reverse-phase HPLC separation. Fractions weremonitored by MALDI MS during separation for the m/z signals of interest.Selected fractions were digested and analyzed by either an AppliedBiosystems 4700 MALDI TOF/TOF (Foster City, Calif.) mass spectrometer ora ThermoLTQ ion trap mass spectrometer (Thermo Electron, San Jose,Calif.). Six proteins were identified including: calcyclin (m/z 10092),dynein light chain 2 (m/z 10262), calpactin I light chain (m/z 11073),astrocytic phosphoprotein PEA-15 (m/z 15035) (FIG. 5C), fatty acidbinding protein 5 (m/z 15076) and tubulin-specific chaperone A (m/z17268). Calcyclin, calpactin I light chain, and tubulin-specificchaperone A were identified as overexpressed in grade IV gliomas. On theother hand, astrocytic phosphoprotein PEA-15 was overexpressed in gradeII and grade III tumors as opposed to grade IV gliomas and fatty acidbinding protein 5 was overexpressed in grade III tumors as opposed tograde N. Calcyclin and dynein light chain 2 also discriminated betweenglioma survival subgroups with calcyclin predominant in STS patients anddynein light chain 2 overexpressed in LTS patients. The presence andrelative expression levels for several of these proteins were verifiedby immunohistochemistry on intact tumor sections. For example, PEA-15 isdemonstrated to be in higher abundance in grade II astrocytomas comparedto grade IV glioblastomas as recognized by the antibody staining pattern(FIG. 5A). This increase in protein expression correlates well with thepresence of a mass spectrometric signal at m/z 15035 collected from aconsecutive grade II tissue section as opposed to the loss of thissignal in the grade IV section (FIG. 5B).

All of the compositions and methods disclosed and claimed herein can bemade and executed without undue experimentation in light of the presentdisclosure. While the compositions and methods of this invention havebeen described in terms of preferred embodiments, it will be apparent tothose of skill in the art that variations may be applied to thecompositions and methods and in the steps or in the sequence of steps ofthe method described herein without departing from the concept, spiritand scope of the invention. More specifically, it will be apparent thatcertain agents which are both chemically and physiologically related maybe substituted for the agents described herein while the same or similarresults would be achieved. All such similar substitutes andmodifications apparent to those skilled in the art are deemed to bewithin the spirit, scope and concept of the invention as defined by theappended claims.

IX. References

The following references, to the extent that they provide exemplaryprocedural or other details supplementary to those set forth herein, arespecifically incorporated herein by reference.

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What is claimed is:
 1. A method of diagnosing or grading a gliomacomprising: (a) subjecting a tissue to mass spectrometry; (b) obtaininga mass spectrometric protein profile from said tissue; (c) comparingsaid mass spectrometric protein profile to a known profile; and (d)diagnosing or grading said tissue based on the similarities anddifferences between said mass spectrometric protein profile and saidknown profile.
 2. The method of claim 1, wherein said mass spectrometryis secondary ion mass spectrometry, laser desorption mass spectrometry,matrix assisted laser desorption mass spectrometry, or electrospray massspectrometry.
 3. The method of claim 1, further comprising obtainingsaid tissue from a patient.
 4. The method of claim 1, further comprisingmaking a treatment decision for a patient from which said tissue wasobtained.
 5. The method of claim 1, wherein diagnosing comprisesdistinguishing non-tumor from grade I, grade II, grade III or grade IVglioma.
 6. The method of claim 1, wherein grading comprisesdistinguishing grade I from grade II, grade III or grade IV glioma. 7.The method of claim 1, wherein grading comprises distinguishing grade IIfrom grade I, grade III or grade IV glioma.
 8. The method of claim 1,wherein grading comprises distinguishing grade III from grade I, gradeII or grade IV glioma.
 9. The method of claim 1, wherein gradingcomprises distinguishing grade IV from grade I, grade II, or grade III.10. The method of claim 1, further comprising assessing one or morepatient variables.
 11. The method of claim 10, wherein patient variablescomprise age, gender, extent of tumor resection, use of pre-surgerychemotherapy, or use of pre-surgery radiotherapy.
 12. The method ofclaim 1, wherein said known profile is a known glioma profile.
 13. Themethod of claim 12, further comprising performing a mass spectrometricanalysis of a known glioma tissue.
 14. The method of claim 1, whereinsaid known profile is a known normal tissue profile.
 15. The method ofclaim 14, further comprising performing a mass spectrometric analysis ofa known normal tissue.
 16. The method of claim 1, further comprisingperforming histologic analysis on said tissue.
 17. The method of claim1, further comprising making a prediction of patient survival based onsaid grading.
 18. The method of claim 1, further comprising making aprediction of drug efficacy based on said grading.
 19. The method ofclaim 1, further comprising making a decision on drug dosing based onsaid grading.
 20. The method of claim 9, further comprising making aprediction of patient survival based on said grading.
 21. A method ofdiagnosing or grading a glioma comprising: (a) assessing glioma tissuefor expression of one or more of calcyclin, dynein light chain 2,calpactin I light chain, astrocytic phosphoprotein PEA-15, fatty acidbinding protein 5 and tubulin-specific chaperone A; (b) comparing saidexpression to a known tissue; and (c) grading said glioma based on thesimilarities and differences between said expression in said glioma andsaid known tissue.
 22. The method of claim 21, wherein assessingcomprises immunodetection, 2-D gel electrophoresis, or massspectrometry.
 23. The method of claim 21, wherein said mass spectrometryis secondary ion mass spectrometry, laser desorption mass spectrometry,matrix assisted laser desorption mass spectrometry, or electrospray massspectrometry.
 24. The method of claim 21, further comprising obtainingsaid glioma tissue from a patient.
 25. The method of claim 21, furthercomprising making a treatment decision for a patient from which saidglioma tissue was obtained.
 26. The method of claim 25, wherein saidtreatment decision involves predicting drug efficacy and or drug dosing.27. The method of claim 21, wherein diagnosing comprises distinguishingnon-tumor from grade I, grade II, grade III or grade IV glioma.
 28. Themethod of claim 21, wherein grading comprises distinguishing grade Ifrom grade II, grade III or grade IV glioma.
 29. The method of claim 21,wherein grading comprises distinguishing grade II from grade I, gradeIII or grade IV glioma.
 30. The method of claim 21, wherein gradingcomprises distinguishing grade III from grade I, grade II or grade IVglioma.
 31. The method of claim 21, wherein grading comprisesdistinguishing grade IV from grade I, grade II, or grade III.
 32. Themethod of claim 21, further comprising assessing one or more patientvariables.
 33. The method of claim 32, wherein patient variablescomprise age, gender, extent of tumor resection, use of pre-surgerychemotherapy, or use of pre-surgery radiotherapy.
 34. The method ofclaim 21, wherein said known tissue is a known glioma tissue.
 35. Themethod of claim 34, further comprising assessing said known gliomatissue for expression of one or more of calcyclin, dynein light chain 2,calpactin I light chain, astrocytic phosphoprotein PEA-15, fatty acidbinding protein 5 and tubulin-specific chaperone A.
 36. The method ofclaim 21, wherein said known tissue is a known normal tissue.
 37. Themethod of claim 36, further comprising assessing said known normaltissue for expression of one or more of calcyclin, dynein light chain 2,calpactin I light chain, astrocytic phosphoprotein PEA-15, fatty acidbinding protein 5 and tubulin-specific chaperone A.
 38. The method ofclaim 21, further comprising performing histologic analysis on saidtissue.
 39. The method of claim 21, further comprising making aprediction of patient survival based on said grading.